A biophysical elucidation for less toxicity of Agglutinin than Abrin-a from the Seeds of Abrus Precatorius in consequence of crystal structure
© Cheng et al; licensee BioMed Central Ltd. 2010
Received: 4 January 2010
Accepted: 30 April 2010
Published: 30 April 2010
X-ray crystal structure determination of agglutinin from abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P41212 with Z = 8, and been refined at 2.6 Å to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 Å and 1.3°. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.
Ribosome inactivating proteins (RIPs) are enzymes that can inactivate ribosomes. The molecular mechanism of inhibitory effect on protein synthesis has been shown that RIPs act as a RNA N-glycosidase hydrolyzing the C-N glycosidic bond of the adenosine residue at position 4324 in rat 28S rRNA [1, 2]. They can cleave the synthetic RNA structure having a short double-helical stem and a loop containing a centered GAGA sequence, the first A being the cleavage site . The depurination inactivates the ribosomes for binding to elongation factor 2 catalyzing GTP hydrolysis and translocation of peptidyl-tRNA to the P site , with a consequence inhibiting the protein synthesis. There are three categories of RIPs according to the physical composition and characteristics. Most commonly RIPs are type I RIPs, only single polypeptide chain proteins composed of the toxophoric A subunit with a molecular mass around 30 kDa [5–8] such as curcin  and trichomislin . Some are type II RIPs consisting of two types of polypeptide subunits, A chain of homologous and functionally similar to type I RIPs and B chain with a galactose-specific lectin domain that binds to cell surfaces, such as ricin  abrin and abrus agglutinin (AAG) . A chain and B chain are from one gene and link through disulfide bond after post-translation modification . Type III RIPs are derived from inactive pro-protein and activated after proteolysis . The mature type III RIPs are two polypeptide subunits acting as an N-glycosidase jointly.
Various RIPs can be isolated from the same plants [15, 16]. Some type II RIPs have been isolated from the beans of the tropical and subtropical leguminous plant Abrus precatorius, jequirity. They are lectins and have an inhibitory effect on the growth of experimental animal tumors [17, 18]. They can be classified as abrins and AAG by oligomerization. Abrins are potent toxic heterodimeric glycoproteins with an LD50 of 20 μg/kg body weight; while AAG is a relatively less toxic heterotetrameric glycoprotein of which the LD50 is 5 mg/kg body weight . But their therapeutics indexes are similar .
The primary structures of abrin-a and AAG were determined [19–21]. AAG had high homology to the extremely toxic ABRa, with 44 (8.0%) similar amino acid residues and 382 (69.8%) invariant amino acid residues. In the A chain of AAG, the 13 amino acid residues with catalytic function among RIPs were completely conserved . The cDNAs of the RIPs isolated from Abrus precatorius have been cloned and their A chains were expressed in Escherichia. coli [21–23]. The amino acid residues at proposed active sites and Pro199 of AAG, which corresponding to Asn200 of abrin-a, were analyzed with site-directed mutagenesis for studying the structure and function of these RIPs [21, 23, 24]. And the results showed that Pro199 in A- (or C-) chain of AAG impair the activity of protein synthesis inhibition because of steric hindrance . According to the biochemical experiments, the mutation of Asn200 on abrin a-chain to Pro200 dramatically decreases the activity than other kind of mutation, including those residues without side-chain, such as Gly [23, 24]. These peculiar results motivate us to crystallize AAG, and make comparison with abrin, since both contains almost identical active pocket, and most important of all, different at Asn200 (the corresponding residue is on AAG Pro199). Bagaria et al.,  reported a 3.5 Å X-ray crystal structure, and proposed the less toxic nature is because of the fewer interactions involved with the substrate adenine.
Bagaria et al.,  assigned their low resolution of AAG crystal to belong to the space group of P42212, instead of our present and previous P41212 , to analyze the crystal structure based on a mixture of indigenous and alien data. They crystallized their Indian AAG material in a condition similar to, but different from ours [25, 26]. Strange to us, they did not determine their own Indian AAG amino acid sequence, but adopted the Taiwanese primary structure [21, 25]. Indian AAG molecular packing may be different from our Taiwanese that could manifest itself some way in different space group. Although they published the controversial paper of 60 kDa structure in advance , this detail worthwhile work of more complicated and precise 120 kDa heterotetramer agglutinin structure spurs the continuous study of our last research .
AAG was isolated from the kernels of Abrus precatorius seeds by chromatographies on a Sepharose 6B column and a Sephadex G-100 column as described previously . The flow rate of chromatography was 20 ml/hr and protein concentration was determined by the bicinchonic acid method . The kernels of 200 g were soaked in 5% cold acetic acid of 1 L overnight and homogenized. After centrifuging at 10,000 g at 4°C for 15 mins, the supernatant was collected for subsequently subjecting to the ammonium sulfate fraction between 35 and 90 and then centrifuging at 10,000 g at 4°C for 20 mins. The precipitate was collected for dialysis against cold 10 mM sodium phosphate buffer, pH 8 at 4°C. The dialysis buffer was changed every 8 hrs for more than 2 days. The supernatant of dialysate was centrifuged at 17,800 g at 4°C for 20 mins and then applied on a Sepharose 6B affinity column (3.0 × 50 cm) pre-equilibrated and washed with 10 mM sodium phosphate buffer, pH 8. The eluent constiting of abrins and AAG were obtained with the elution buffer, the wash buffer containing 100 mM D-galactose. Then the precipitate was obtained from the eluent subjected to 90% ammonium sulfate and dialyzed and centrifuged as mentioned above. The supernatant was loaded onto gel filtration on Sephadex G-100 column (2.2 × 100 cm) with 10 mM sodium phosphate buffer, pH 8. Two major peaks can be observed and the fractions of AAG, corresponding to the first peak, were pooled and lyophilized.
The formula for crystallization was described in our previous paper . Crystals suitable for X-ray analysis were obtained by the sitting drop vapor-diffusion method at room temperature (297 (2) K) . 8 μl of protein solution at a concentration of 10 mg/ml prepared from lyophilized protein was mixed with 8 μl of reservoir solution containing PEG 8000; the precipitant condition was 0.1 M Tris pH 7.5 with 6.5% PEG 8000 plus 1% sodium azide and crystals appeared after nearly four months.
X-ray Data were collected with a crystal of dimensions 0.30 × 0.30 × 0.25 mm that was mounted in a cryo-loop manufactured by Hampton Research. After immersed in the cryo-protectant of 20% glycerol and 80% mother liquor for several seconds, the cryo-loop was mounted on goniometer head inside liquid nitrogen stream at 100 K. X-ray diffraction was measured with CCD (ADSC Quantum-Q4R CCD Area Detector), on 1 D synchrotron radiation X-ray (SPring-8 Taiwan Contract Beam-line BL12B2 of NSRRC). The crystal-to-detector distance was 215 mm. The space group and unit-cell parameters were determined from the well resolved diffraction spots. The data were processed using the programs HKL2000 . The agglutinin crystal belongs to the tetragonal system, with unit-cell parameters a = b = 137.05, c = 214.42 Å, V = 4.0275 × 106 Å3, Z = 8. A 99.1% complete dataset to 2.47 Å resolution of 73,976 unique reflections was collected with averaged Rsym of 7.2%, averaged χ2 of 1.153, averaged I/σ of 11.89, and redundancy of 4.1.
Determination of space group and initial phase
The systematic absences, l = 4n + 1, 2, 3 for 00l reflections, and h = 2n + 1 for h00 reflections, indicate that there are two possible space groups, namely P41212 or P43212. The ambiguity of space group was solved together with the initial phase problem by molecular replacement method using version 1.1 of CNS program  with the coordinates of abrin-a  as model. An X-ray diffraction data shell from 4 to 15 Å was used for the calculation of the cross rotation function with CNS program . The highest two were corresponding to a rotation of the model by the rotation angel of θ1 = 37.9E, θ2 = 39.6E, θ3 = 342.1E, and θ1 = 358.1E, θ2 = -0.5E, θ3 = 2.4E in the space group of P41212. After translation searches with CNS program  according to these two rotation angles, the initial model of AB- and CD-chains of agglutinin was established.
Crystal data and refinement statistics for AAG.
X-ray wavelength (Å)
Space group name
Cell length a (Å)
Cell length b (Å)
Cell length c (Å)
Cell volume (Å^3)
Cell formula units Z
Cell measurement temperature (K)
Crystal size (mm^3)
0.30 × 0.30 × 0.25
Colvent content (%)
Matthews coefficient (Å^3/Da)
Averaged R_sym (outer sell)
Averaged I/FI (outer sell)
Completeness (%) (outer sell)
Redundancy (outer sell)
Resolution range of collection (Å)
2.47 ~ 30.0
Resolution range of refinement (Å)
2.6 ~ 19.88
R_cryst (outer sell)
R_free (outer sell)
No. of protein atoms
No. of water molecules
No. of NAG atoms
rms deviation from ideal bond length (Å)
rms deviation from ideal bond angle (º)
Isotropic thermal factor restraints
Main chain bond (Å^2)
Main chain angle (Å^2)
Side chain bond (Å^2)
Side chain angle (Å^2)
Ramachandran plot  (% of residues)
in the most favored regions (A, B, L)
in the additionally allowed regions (a, b, l, p)
The program SPHGEN identifies the active site, and other sites of interest, and generates the sphere centers that fill the site. It has been described in the original paper . The program GRID generates the scoring grids [40, 41]. Within the DOCK suite of programs, the program DOCK matches spheres (generated by SPHGEN) with ligand atoms and uses scoring grids (from GRID) to evaluate ligand orientations [38, 39]. Program DOCK also minimizes energy based scores . Parameters used in DOCK were modified from the paper of protein docking and complementary principle .
The atomic coordinates of the refined agglutinin structure and the reflection data have been deposited with the Protein Data Bank in Japan. The accession numbers for these atomic coordinates are (PDB ID) 2ZR1and (RCSB ID) RCSB028317.
Results and Discussion
Structure of the AAG A(or C)-chain
Structure of the AAG B (or D)-chain
The overall folding of the AAG B (or D)-chain and the abrin-a B-chain is very similar, as shown in figure 1, and the disulfide bond connecting A- and B-chains is conserved. The α-carbon traces of their N terminal, residues 1 to 12 differ significantly. The first four residues in the AAG B (or D)-chain are severely disordered, and we could not determine their structures by X-ray diffraction. The AAG B-chain is composed of two homologous domains, δ1 and δ2, mainly formed by β-sheets and loops. Figure 4 shows the sequence and secondary structures, while figure 5 shows the cartoon of the two domains. Domain δ1 (figure 5(a)), composed of residues 5 to 140, consists of five anti-parallel β-sheets, one 4-stranded (of ijkl), one 3-stranded (of aef), and three 2-stranded (strands bm, cd, and gh respectively), and one α-helix of residues 90 to 94. The strands and helices alternate in the order abcdefghAijklm. Domain δ2 (figure 5(b)), composed of residues 141 to 267, consists of four anti-parallel β-sheets, including two 4-stranded (strands ynqr and uvwx respectively), and two 2-stranded (strands op and st) sheets.
Structure of Active site
Quaternary Structure of AAG
Hydrogen bonds between inter-subunit with symmetry-related AA' and CC' chains.
A Gln 121 NE2
A Gln121 NE2
A Arg 25 NH1
A Leu 130 N
A Leu 130 N
A Arg 134 NH2
A'Asn 180 O
A Arg 134 NH2
A'Asn 180 O
A Arg 134 NE
A'Asn 181 O
A Arg 134 NE
A'Asn 181 O
A Gln 135 NE2
A'Ser 127 OG
A Gln 135 NE2
A'Ser 127 OG
C Gln 121 NE2
C'Ser 145 O
C Gln 121 NE2
C'Ser 145 O
C Ser 127 OG
C'Gly 143 N
C Ser 127 OG
C'Gly 143 N
C Arg 134 NR
C' Arg 134 NR
C Tyr57 OH
C Gln 135 NE2
C' Gln 135 NE2
C Gln135 O
C Ser 145 N
C' Ser 145 N
C Gln121 O
Docking of 28SRNA to AAG and Abrin-a
We want to explore whether the difference in the critical residue, bring any change in structure. However, we could not observe significant main-chain distortion due to the difference in the 200 residue on higher resolution structure. Hence, the reason for the lower toxicity of agglutinin than abrin-a might be due to the deformation from inactive to active state of abrin depends on the meta-stable huge helix, composed of helix h and helix g. The mutation of Asn200 to Pro200 destroys the mechanism.
We have successfully solved the structure of 120 kDa heterotetramer agglutinin AB and CD chains, and reduced the R-factor to 20.4% at 2.6 Å resolution data. Ten disulfide bonds, three N-acetylglucosamines, and 169 water molecules were found in the successive (2Fo-Fc) map. 22 hydrogen bonds between A (or C)-chain and symmetry-related A' (or C') were found. Water molecules were not found in the Bagaria's paper and no subsequent hydrogen bond lengths were listed based on their lower resolution structure . Docking study revealed that due to Pro199, agglutinin is unable to form a critical hydrogen bond with G4323 of 28SRNA, which is found in the docking result of abrin-a. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.
observed structure factor
calculated structure factor
protein data bank.
The authors thank Mr Shyh-Ming Chen for setting up the computing programs. They also thank to the National Science Council of Taiwan for financial support. They are indebted to SPring-8 and the National Synchrotron Radiation Research Center for data collection.
- Endo Y, Misui K, Motizuki K, Tsurugi K: The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes. The site and the characteristics of the modification in 28 S ribosomal RNA caused by the toxins. J Biol Chem. 1987, 262: 5908-5912.PubMedGoogle Scholar
- Endo Y, Tsurugi K: RNA N-glycosidase activity of ricin A-chain Mechanism of action of the toxic lectin ricin on eukaryotic ribosomes. J Biol Chem. 1987, 262: 8128-8130.PubMedGoogle Scholar
- Endo Y, Gluck A, Wool IG: Ribosomal RNA identity elements for ricin A-chain recognition and catalysis. J Mol Biol. 1991, 221: 193-207. 10.1016/0022-2836(91)80214-F.View ArticlePubMedGoogle Scholar
- Jimenez A, Vazquez DC: Plant and Fungal Protein and Glycoprotein Toxins Inhibiting Eukaryote Protein Synthesis. Annu Rev Microbiol. 1985, 39: 649-672. 10.1146/annurev.mi.39.100185.003245.View ArticlePubMedGoogle Scholar
- Barbieri L, Stirpe F: Ribosome-inactivating proteins from plants: properties and possible uses. Cancer Surv. 1982, 1: 489-520.Google Scholar
- Stirpe F, Barbieri L, Battelli MG, Soria M, Lappi DA: Ribosome-inactivating proteins leads to increased fungal protection in transgenic tobacco plants. Bio-Technology. 1992, 10: 405-412.View ArticlePubMedGoogle Scholar
- Hartley MR, Lord JM: Cytotoxic ribosome-inactivating lectins from plants. Biochim Biophys Acta. 2004, 1701: 1-14.View ArticlePubMedGoogle Scholar
- Olsnes S: The history of ricin abrin and related toxins. Toxicon. 2004, 44: 361-370. 10.1016/j.toxicon.2004.05.003.View ArticlePubMedGoogle Scholar
- Lin J, Chen Y, Xu Y, Yan F, Tang L, Chen F: Cloning and expression of curcin a ribosome inactivating protein from the seeds of jatropha curcas. Acta Botanica Sinica. 2003, 45: 858-863.Google Scholar
- Mi SL, An CC, Wang Y, Chen JY, Che NY, Gao Y, Chen ZL: Trichomislin a novel ribosome-inactivating protein a novel ribosome-inactivating protein induces apoptosis that involves mitochondria and caspase-3. Archives of Biochemistry and Biophysics. 2005, 434: 258-265. 10.1016/j.abb.2004.11.009.View ArticlePubMedGoogle Scholar
- Olsnes S, Phil A: Different biological properties of the two constituent peptide chains of ricin a toxic protein inhibiting protein synthesis. Biochemistry. 1973, 12: 3121-3126. 10.1021/bi00740a028.View ArticlePubMedGoogle Scholar
- Lin JY, Lee TC, Hsu ST, Tung TC: Isolation of four isotoxic proteins and one agglutinin from jequiriti bean (Abrus precatorius). Toxicon. 1981, 19: 41-51. 10.1016/0041-0101(81)90116-1.View ArticlePubMedGoogle Scholar
- Lord JM: Synthesis and intracellular transport of lectin and storage protein precursors in endosperm from castor bean. Eur J Biochem. 1985, 146: 403-409. 10.1111/j.1432-1033.1985.tb08666.x.View ArticlePubMedGoogle Scholar
- Mundy J, Leah R, Boston R, Endo Y, Stirpe F: Genes encoding ribosome-inactivating proteins. Plant Mol Biol Rep. 1994, 12: 60-62. 10.1007/BF02671573.View ArticleGoogle Scholar
- Leah R, Tommerup H, Svendsen I, Mundy J: Biochemical and molecular characterization of three barley seed proteins with antifungal properties. J Biol Chem. 1991, 266: 1564-1573.PubMedGoogle Scholar
- Desvoyes B, Poyet JL, Schlick JL, Adami P, Jouvenot M, Dulieu P: Identification of a biological inactive complex form of pokeweed antiviral protein. FEBS Lett. 1997, 410: 303-308. 10.1016/S0014-5793(97)00648-0.View ArticlePubMedGoogle Scholar
- Olsnes S, Phil A: In Receptors and Recognition Series: The Specificity and Action of Animal. Bacterial and Plant Toxins. Edited by: Cuatrecasas P. 1982, Chapman and Hall, London, 31-131.Google Scholar
- Lin JY, Li JS, Tung TC: Lectin Derivatives of Methotrexate and Chlorambucil as Chemotherapeutic Agents. J Natl Cancer Inst. 1981, 66: 523-528.PubMedGoogle Scholar
- Funatsu G, Taguchi Y, Kamenosno M, Yanaka M: The complete amino acid sequence of the A-chain of abrin-a a toxic protein from the seeds of Abrus precatorius. Agric Biol Chem. 1988, 52: 1095-1097.View ArticleGoogle Scholar
- Chen YL, Chow LP, Tsugita A, Lin JY: The complete primary structure of abrin-a B chain. FEBS Lett. 1992, 309: 115-118. 10.1016/0014-5793(92)81076-X.View ArticlePubMedGoogle Scholar
- Liu CL, Tsai CC, Lin SC, Wang LI, Hsu CI, Hwang MJ, Lin JY: Primary Structure and Function Analysis of the Abrus precatorius Agglutinin A Chain by Site-directed Mutagenesis. J Biol Chem. 2000, 275: 1897-1901. 10.1074/jbc.275.3.1897.View ArticlePubMedGoogle Scholar
- Hung CH, Lee MC, Lee TC, Lin JY: Primary Structure of Three Distinct Isoabrins Determined by cDNA Sequencing: Conservation and Significance. J Mol Biol. 1993, 229: 263-267. 10.1006/jmbi.1993.1029.View ArticlePubMedGoogle Scholar
- Hung CH, Lee MC, Chen JK, Lin JY: Cloning and expression of three abrin A-chains and their mutants derived by site-specific mutagenesisin Escherichia coli. Eur J Biochem. 1994, 219: 83-87. 10.1111/j.1432-1033.1994.tb19917.x.View ArticlePubMedGoogle Scholar
- Chen JK, Hung CH, Liaw YC, Lin JY: Identification of amino acid residues of abrin-a A chain is essential for catalysis and reassociation with abrin-a B chain by site-directed mutagenesis. Protein Engineering. 1997, 10: 827-833. 10.1093/protein/10.7.827.View ArticlePubMedGoogle Scholar
- Bagaria A, Surendranath K, Ramagopal UA, Ramakumar S, Karande AA: Structure-Function Analysis and Insights into the Reduced Toxicity of Abrus precatorius Agglutinin I in Relation to Abrin. J Biol Chem. 2006, 281: 34465-34474. 10.1074/jbc.M601777200.View ArticlePubMedGoogle Scholar
- Panneerselvam K, Lin SC, Liu CL, Liaw YC, Lin JY, Lu TH: Crystallization of agglutinin from the seeds of Abrus precatorius. Acta Cryst. 2000, D56: 898-899.Google Scholar
- Smith PK, Krohn RI, Hermanson GT, Mallia AK, Gartner FH, Provenzano MD, Fujimoto EK, Goeke NM, Olson BJ, Klenk DC: Measurement of protein using bicinchoninic acid. Anal Biochem. 1985, 150: 76-85. 10.1016/0003-2697(85)90442-7.View ArticlePubMedGoogle Scholar
- McPherson A: Preparation and Analysis of Protein Crystals. 1982, John Wiley & Sons New York USA, 94-96. 115Google Scholar
- Otwinowski Z, Minor W: Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods in Enzymology. Macromolecular Crystallography part A. 1997, 276: 307-326. full_text.View ArticleGoogle Scholar
- Brunger AT, Adams PD, Clore GM, Delano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL: Crystallography & NMR system: A new software system for macromolecular structure determination. Acta Cryst. 1998, D54: 905-921.Google Scholar
- Tahirov TH, Lu TH, Liaw YC, Chen YL, Lin JY: Crystal Structure of Abrin-a at 2.14 D. J Mol Biol. 1995, 250: 354-367. 10.1006/jmbi.1995.0382.View ArticlePubMedGoogle Scholar
- DeLano WL, Brunger AT: The Direct Rotation Function: Rotational Patterson Correlation Search Applied to Molecular Replacement. Acta Cryst. 1995, D51: 740-748.Google Scholar
- Brunger AT: Extension of molecular replacement: A new search strategy based on Patterson correlation refinement. Acta Cryst. 1990, A46: 46-57.View ArticleGoogle Scholar
- Brunger AT: The Free R Value: a Novel Statistical Quantity for Assessing the Accuracy of Crystal Structures. Nature. 1992, 355: 472-474. 10.1038/355472a0.View ArticlePubMedGoogle Scholar
- Brunger AT, Krukowski A, Erickson J: Slow-Cooling Protocols for Crystallographic Refinement by Simulated Annealing. Acta Cryst. 1990, A46: 585-593.View ArticleGoogle Scholar
- Abrahams JP, Leslie AG W: Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Cryst. 1996, D52: 30-42.Google Scholar
- Jones TA, Zou JY, Cowan SW, Kjeldgaard M: Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Cryst. 1991, A47: 110-119.View ArticleGoogle Scholar
- Adams PD, Pannu NS, Read RJ, Brunger AT: Cross-validated Maximum Likelihood Enhances Crystallographic Simulated Annealing Refinement. Proc Natl Acad Sci USA. 1997, 94: 5018-5023. 10.1073/pnas.94.10.5018.PubMed CentralView ArticlePubMedGoogle Scholar
- Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE: A geometric approach to macromolecule-ligand interactions. J Mol Biol. 1982, 161: 269-288. 10.1016/0022-2836(82)90153-X.View ArticlePubMedGoogle Scholar
- Shoichet BK, Bodian DL, Kuntz ID: Molecular docking using shape descriptors. J Comp Chem. 1992, 13: 380-397. 10.1002/jcc.540130311.View ArticleGoogle Scholar
- Meng EC, Shoichet BK, Kuntz ID: Automated docking with grid-based energy evaluation. J Comp Chem. 1992, 13: 505-524. 10.1002/jcc.540130412.View ArticleGoogle Scholar
- Meng EC, Gschwend DA, Blaney JM, Kuntz ID: Orientational sampling and rigid-body minimization in molecular docking. Proteins. 1993, 17: 266-278. 10.1002/prot.340170305.View ArticlePubMedGoogle Scholar
- Shoichet BK, Kuntz ID: Protein docking and complementarity. J Mol Biol. 1991, 221: 327-346. 10.1016/0022-2836(91)80222-G.View ArticlePubMedGoogle Scholar
- Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C: The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucl Acids Res. 2005, D247-D251. 33 Database
- Rutenber E, Robertus JD: Structure of ricin B-chain at 2.5 Å resolution. Proteins Struct Func Genet. 1991, 10: 260-269. 10.1002/prot.340100310.View ArticleGoogle Scholar
- Krissinel E, Henrick K: Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007, 372: 774-797. 10.1016/j.jmb.2007.05.022.View ArticlePubMedGoogle Scholar
- Correll CC, Munishkin A, Chan YL, Ren Z, Wool IG, Steitz TA: Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proc Natl Acad Sci USA. 1998, 95: 13436-13441. 10.1073/pnas.95.23.13436.PubMed CentralView ArticlePubMedGoogle Scholar
- Weston SA, Tucker AD, Thatcher DR, Derbyshire DJ, Pauptit RA: X-ray structure of recombinant ricin A-chain at 1.8 Å resolution. J Mol Biol. 1994, 244: 410-422. 10.1006/jmbi.1994.1739.View ArticlePubMedGoogle Scholar
- Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE: UCSF Chimera - A Visualization System for Exploratory Research and Analysis. J Comput Chem. 2004, 25: 1605-1612. 10.1002/jcc.20084.View ArticlePubMedGoogle Scholar
- Laskowski RA, MacArthur MW, Moss DS, Thornton JM: PROCHECK: a program to check the stereochemical quality of protein structures. J App Cryst. 1993, 26: 283-291. 10.1107/S0021889892009944.View ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.