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7th3

Single-domain VHH intrabodies neutralize ricin toxin

Method: X-RAY DIFFRACTION Dmax: 78.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ricin chain A

Ricinus communis

UniProt P02879

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 36–302 Not recorded VHH antibody × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；418 mM ammonium chloride, 22% PEG 3350 Resolution 2.29 Å R-free 0.272

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7TH3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BR5 RICIN A CHAIN (RECOMBINANT) COMPLEX WITH NEOPTERIN Deposited 1998-08-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded NEO NEOPTERIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.9；pH 8.9
Resolution 2.50 Å
1BR6 RICIN A CHAIN (RECOMBINANT) COMPLEX WITH PTEROIC ACID Deposited 1998-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–302（268 aa）
Not recorded PT1 PTEROIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.9；pH 8.9
Resolution 2.30 Å
1IFS RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH ADENOSINE (ADENOSINE BECOMES ADENINE IN THE COMPLEX) Deposited 1996-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–298（261 aa） Fragment：A CHAIN
Mutation：I1M, F2V ADE ADENINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1IFT RICIN A-CHAIN (RECOMBINANT) Deposited 1996-07-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–298（261 aa） Fragment：A CHAIN
Mutation：I1M, F2V No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1IFU RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH FORMYCIN Deposited 1996-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–298（261 aa） Fragment：A CHAIN
Mutation：I1M, F2V FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1IL3 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 7-DEAZAGUANINE Deposited 2001-05-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded 7DG 7-DEAZAGUANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；277 K；PEG 8000, TRIS-HCL, BETA-MERCAPTOETHANOL, EDTA, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.80 Å R-free 0.273
1IL4 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 9-DEAZAGUANINE Deposited 2001-05-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded 9DG 9-DEAZAGUANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；277 K；PEG 8000, TRIS-HCL, BETA-MERCAPTOETHANOL, EDTA, 9-DEAZAGUANINE, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.293
1IL5 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE (DDP) Deposited 2001-05-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded DDP 2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；277 K；PEG 8000, TRIS-HCL, BETA-MERCAPTOETHANOL, EDTA, 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.80 Å R-free 0.283
1IL5 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE (DDP) Deposited 2001-05-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–302（267 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；277 K；PEG 8000, TRIS-HCL, BETA-MERCAPTOETHANOL, EDTA, 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.80 Å R-free 0.283
1IL9 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 8-METHYL-9-OXOGUANINE Deposited 2001-05-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded MOG 5-AMINO-2-METHYL-6H-OXAZOLO[5,4-D]PYRIMIDIN-7-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；277 K；PEG 8000, TRIS-HCL, BETA-MERCAPTOETHANOL, EDTA, 8-METHYL-9-OXOGUANINE, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.10 Å R-free 0.306
1J1M Ricin A-Chain (Recombinant) at 100K Deposited 2002-12-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Mutation：N137D SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.9M Ammomium Sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.50 Å R-free 0.213
1OBS STRUCTURE OF RICIN A CHAIN MUTANT Deposited 1996-06-25 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Mutation：R180H No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1OBT STRUCTURE OF RICIN A CHAIN MUTANT, COMPLEX WITH AMP Deposited 1996-06-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Mutation：R180H AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1RTC THE STRUCTURE OF RECOMBINANT RICIN A CHAIN AT 2.3 ANGSTROMS Deposited 1992-10-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1UQ4 RICIN A-CHAIN (RECOMBINANT) R213D MUTANT Deposited 2003-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 40–302（263 aa） Fragment：A CHAIN, RESIDUES 40-302
Mutation：YES SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.2；SEE REFERENCE 1, pH 4.20
Resolution 1.90 Å R-free 0.231
1UQ5 RICIN A-CHAIN (RECOMBINANT) N122A MUTANT Deposited 2003-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 40–302（263 aa） Fragment：A CHAIN, RESIDUES 40-302
Mutation：YES ACT ACETATE ION × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.2；SEE REFERENCE 1, pH 4.20
Resolution 1.40 Å R-free 0.214
2AAI Crystallographic refinement of ricin to 2.5 Angstroms Deposited 1993-09-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
2P8N Ricin a-chain (recombinant) complex with adenine Deposited 2007-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa） Fragment：residues 36-302
Not recorded SO4 SULFATE ION × 3 ADE ADENINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；295 K；20% AMMONIUM SULFATE, 50 MIMILLIMOLAR SODIUM ACETATE, PH 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K, pH 4.20
Resolution 1.94 Å R-free 0.301
2PJO Ricin a-chain (recombinant) complex with n-methylurea Deposited 2007-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded SO4 SULFATE ION × 2 NMU N-METHYLUREA × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；295 K；AMMONIUM SULFATE, SODIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K, pH 4.20
Resolution 1.80 Å R-free 0.247
2R2X Ricin A-chain (recombinant) complex with Urea Deposited 2007-08-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded SO4 SULFATE ION × 2 URE UREA × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；295 K；Ammonium sulfate, sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.40 Å R-free 0.297
2R3D Ricin A-chain (recombinant) complex with Acetamide Deposited 2007-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa） Fragment：Unp residues 36-302
Not recorded SO4 SULFATE ION × 2 ACM ACETAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；295 K；Ammonium sulfate, sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.09 Å R-free 0.272
2VC3 Ricin A-Chain (Recombinant) E177D Mutant with a bound acetate Deposited 2007-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa） Fragment：RESIDUES 36-302
Mutation：YES ACT ACETATE ION × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.2；pH 4.2
Resolution 1.60 Å R-free 0.209
2VC4 Ricin A-Chain (Recombinant) E177D Mutant Deposited 2007-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa） Fragment：RESIDUES 36-302
Mutation：YES GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.2；pH 4.2
Resolution 1.39 Å R-free 0.199
3EJ5 complex of Ricin A chain and pyrimidine-based inhibitor Deposited 2008-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 40–296（257 aa） Fragment：sequence database residues 40-296
Not recorded EJ5 4-[3-(2-amino-4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)propyl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；277 K；tris-HCl, BME, EDTA, PEG 8000, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.50 Å R-free 0.266
3HIO Crystal structure of Ricin A-chain in complex with the cyclic tetranucleotide inhibitor, a transition state analogue Deposited 2009-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded C2X 9,9'-{(2R,3R,3aR,5S,7aR,9R,10R,10aR,12S,23R,25aR,27R,28R,28aR,30S,32aR,35aR,37S,39aR)-9-(6-amino-9H-purin-9-yl)-34-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-5,12,23,30,37-pentahydroxy-3,10,28-trimethoxy-5,12,23,30,37-pentaoxidotetracosahydro-2H,7H,25H-trifuro[3,2-f:3',2'-l:3'',2''-x]pyrrolo[3,4-r][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]undecaoxazapentaphosphacyclopentatriacontine-2,27-diyl}bis(2-amino-3,9-dihydro-6H-purin-6-one) × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；25% PEG2000, 0.2M Lithium sulfate, 0.1M Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.00 Å R-free 0.254
3LC9 Ricin A-chain variant 1-33/44-198 with engineered disulfide bond Deposited 2010-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–233（198 aa）
Mutation：R48C, T77C SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；290 K；Protein buffer: 50mM MES pH 6.4, 200mM NaCl Crystallization Solution: 0.17M Ammonium Sulfate, 25.5% w/v PEG 4000, 15% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.28 Å R-free 0.245
3MK9 Stabilized Ricin Immunogen 1-33/44-198 Deposited 2010-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–233（198 aa）
Mutation：V49C, E99C SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；290 K；Protein Buffer: 50mM MES pH 6.4, 200mM NaCl, 2mM BME, Crystallization Solution: 0.17M Ammonium Sulfate, 25.5% w/v PEG 4000, 15% v/v Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.08 Å R-free 0.236
3RTI Crystal structure of ricin bound with formycin monophosphate Deposited 2011-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa） Fragment：Ricin A chain
Chain B 315–576（262 aa） Fragment：Ricin B chain
Not recorded FMP FORMYCIN-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions batch；pH 4.75；298 K；11.5% PEG 8000, 0.05 M sodium acetate, 2 mM lactose, pH 4.75, batch, temperature 298K
Resolution 2.80 Å
3RTJ Crystal structure of ricin bound with dinucleotide ApG Deposited 2011-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions batch；pH 4.75；298 K；11.5% PEG 8000, 0.05 M sodium acetate, 2 mM lactose, pH 4.75, batch, temperature 298K
Resolution 3.00 Å
3SRP Structure of Rivax: A Human Ricin Vaccine Deposited 2011-07-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Mutation：V76M, Y80A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；290 K；30% Ammonium Sulfate, 50 mM Sodium Acetate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.14 Å R-free 0.254
4ESI Structure of ricin A chain bound with N-((1H-1,2,3-triazol-4-yl)methyl-2-amino-4-oxo-3,4-dihydropteridine-7-carboxamide Deposited 2012-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded 0RB 2-amino-4-oxo-N-(1H-1,2,3-triazol-5-ylmethyl)-1,4-dihydropteridine-7-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.87 Å R-free 0.285
4HUO Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanine Deposited 2012-11-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 36–302（267 aa）
Not recorded RS8 N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M Ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.52 Å R-free 0.230
4HUO Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanine Deposited 2012-11-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 36–302（267 aa）
Not recorded RS8 N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M Ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.52 Å R-free 0.230
4HUP Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanyl)-L-phenylalanine Deposited 2012-11-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 36–302（267 aa）
Not recorded 19M (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-3-phenyl-propanoic acid × 1 SO4 SULFATE ION × 2 MLA MALONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.236
4HUP Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanyl)-L-phenylalanine Deposited 2012-11-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 36–302（267 aa）
Not recorded 19M (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-3-phenyl-propanoic acid × 2 SO4 SULFATE ION × 4 MLA MALONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.236
4HV3 Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonyl-L-serinyl)-L-tryptophan Deposited 2012-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded 19L (2S)-2-[[(2S)-2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]-3-oxidanyl-propanoyl]amino]-3-(1H-indol-3-yl)propanoic acid × 1 SO4 SULFATE ION × 1 MLA MALONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M Ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.54 Å R-free 0.231
4HV7 Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)glycine Deposited 2012-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 36–302（267 aa）
Not recorded 19J 2-[2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]ethanoylamino]ethanoic acid × 1 SO4 SULFATE ION × 1 MLA MALONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.87 Å R-free 0.236
4HV7 Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)glycine Deposited 2012-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 36–302（267 aa）
Not recorded 19J 2-[2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]ethanoylamino]ethanoic acid × 2 SO4 SULFATE ION × 2 MLA MALONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.87 Å R-free 0.236
4IMV Ricin A-chain variant 1-33/44-198 with engineered disulfide bond, R48C/T77C/D75N Deposited 2013-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–233（198 aa） Fragment：unp residues 36-233
Mutation：R48C, T77C, D75N SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；290 K；0.17 M Ammonium Sulfate, 25.5% (w/v) Peg 4000, 15% Glycerol , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.25 Å R-free 0.242
4KUC Crystal structure of ricin-A chain in complex with the antibody 6C2 Deposited 2013-05-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–302（267 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.1M Nacitrate,ph 5.0, 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.79 Å R-free 0.289
4KUC Crystal structure of ricin-A chain in complex with the antibody 6C2 Deposited 2013-05-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 36–302（267 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.1M Nacitrate,ph 5.0, 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.79 Å R-free 0.289
4LGP Ricin A chain bound to camelid nanobody (VHH1) Deposited 2013-06-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–296（261 aa） Fragment：UNP residues 36-296
Not recorded CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；100 mM Bicine, 20 % PEG 6000, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 2.40 Å R-free 0.281
4LGP Ricin A chain bound to camelid nanobody (VHH1) Deposited 2013-06-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 36–296（261 aa） Fragment：UNP residues 36-296
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；100 mM Bicine, 20 % PEG 6000, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 2.40 Å R-free 0.281
4LGR Ricin A chain bound to camelid nanobody (VHH3) Deposited 2013-06-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–294（255 aa） Fragment：UNP residues 40-294
Not recorded ZN ZINC ION × 3 ACY ACETIC ACID × 2 CL CHLORIDE ION × 8 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；293 K；100 mM NaAcetate, 200 mM Zinc Acetate, 10% PEG 3000, pH 4.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.65 Å R-free 0.204
4LGS Ricin A chain bound to camelid nanobody (VHH4) Deposited 2013-06-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 39–301（263 aa） Fragment：UNP residues 39-301
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；100 mM NaHepes, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, temperature 293K
Resolution 2.70 Å R-free 0.248
4LHJ Ricin A chain bound to camelid nanobody (VHH5) Deposited 2013-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 39–297（259 aa） Fragment：UNP residues 39-297
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；293 K；100 mM NaAcetate, 200 mM NaCl, 40% PEG 300, pH 4.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.80 Å R-free 0.250
4LHQ Ricin A chain bound to camelid nanobody (VHH8) Deposited 2013-07-01 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 39–298（260 aa） Fragment：UNP residues 39-298
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；100 mM NaAcetate, 2 M NaFormate, pH 4.6, VAPOR DIFFUSION, temperature 293K
Resolution 2.30 Å R-free 0.248
4LHQ Ricin A chain bound to camelid nanobody (VHH8) Deposited 2013-07-01 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 39–298（260 aa） Fragment：UNP residues 39-298
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；100 mM NaAcetate, 2 M NaFormate, pH 4.6, VAPOR DIFFUSION, temperature 293K
Resolution 2.30 Å R-free 0.248
4MX1 Structure of ricin A chain bound with 2-amino-4-oxo-N-(2-(3-phenylureido)ethyl)-3,4-dihydropteridine-7-carboxamide Deposited 2013-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded 1MX 2-amino-4-oxo-N-{2-[(phenylcarbamoyl)amino]ethyl}-3,4-dihydropteridine-7-carboxamide × 1 SO4 SULFATE ION × 1 MLA MALONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.59 Å R-free 0.261
4MX5 Structure of ricin A chain bound with benzyl-(2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)ethyl)carbamate Deposited 2013-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 36–302（267 aa）
Not recorded 5MX benzyl (2-{[(2-amino-4-oxo-3,4-dihydropteridin-7-yl)carbonyl]amino}ethyl)carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.52 Å R-free 0.245
4Q2V Crystal Structure of Ricin A chain complexed with Baicalin inhibitor Deposited 2014-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa） Fragment：Ricin A chain
Not recorded 0XE 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl beta-D-glucopyranosiduronic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.2M ammonium sulphate, 0.1M sodium acetate, 10% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.243
4Z9K Ricin A chain bound to camelid nanobody (VHH2)(F5) Deposited 2015-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 39–296（258 aa） Fragment：UNP residues 39-296
Not recorded EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；100 mM Tris, 15% PEG 3000, 2 mM Zinc acetate, 10 mM sulfobetaine
Resolution 1.50 Å R-free 0.195
5BOZ Ricin A chain bound to camelid nanobody (VHH9)(E1) Deposited 2015-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 39–299（261 aa） Fragment：UNP residues 39-298
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.45 M Ammonium Sulfate, 25% glycerol
Resolution 3.10 Å R-free 0.277
5BOZ Ricin A chain bound to camelid nanobody (VHH9)(E1) Deposited 2015-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 39–299（261 aa） Fragment：UNP residues 39-298
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.45 M Ammonium Sulfate, 25% glycerol
Resolution 3.10 Å R-free 0.277
5BOZ Ricin A chain bound to camelid nanobody (VHH9)(E1) Deposited 2015-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 39–299（261 aa） Fragment：UNP residues 39-298
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.45 M Ammonium Sulfate, 25% glycerol
Resolution 3.10 Å R-free 0.277
5BOZ Ricin A chain bound to camelid nanobody (VHH9)(E1) Deposited 2015-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 39–299（261 aa） Fragment：UNP residues 39-298
Not recorded SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.45 M Ammonium Sulfate, 25% glycerol
Resolution 3.10 Å R-free 0.277
5BOZ Ricin A chain bound to camelid nanobody (VHH9)(E1) Deposited 2015-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 39–299（261 aa） Fragment：UNP residues 39-298
Not recorded SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.45 M Ammonium Sulfate, 25% glycerol
Resolution 3.10 Å R-free 0.277
5BOZ Ricin A chain bound to camelid nanobody (VHH9)(E1) Deposited 2015-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 39–299（261 aa） Fragment：UNP residues 39-298
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.45 M Ammonium Sulfate, 25% glycerol
Resolution 3.10 Å R-free 0.277
5DDZ Crystal structure of the RTA-c10-P2 complex Deposited 2015-08-25 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.4 M ammonium dihydrogen phosphate
Resolution 1.50 Å R-free 0.175
5E1H Ricin toxin in complex with neutralizing single chain monoclonal antibodies (VHHs) Deposited 2015-09-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–297（258 aa）
Not recorded CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；100 mM BisTris pH 5.5, 25% PEG 3000, 260 mM NaCl, and 10 mM Tris (2carboxyethyl)phosphine hydrochloride
Resolution 2.03 Å R-free 0.257
5GU4 rRNA N-glycosylase RTA Deposited 2016-08-24 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa） Fragment：UNP residues 36-302
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2.8 M sodium acetate, tetrahydrate pH7.0 30%-35% glucose
Resolution 1.55 Å R-free 0.255
5GU4 rRNA N-glycosylase RTA Deposited 2016-08-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–302（267 aa） Fragment：UNP residues 36-302
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2.8 M sodium acetate, tetrahydrate pH7.0 30%-35% glucose
Resolution 1.55 Å R-free 0.255
5J56 RTA-V1C7 Deposited 2016-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa） Fragment：UNP residues 40-294
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 ACY ACETIC ACID × 2 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate pH 4.6 and 8% PEG4000
Resolution 1.80 Å R-free 0.210
5J57 V5E1-RTA complex Deposited 2016-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa） Fragment：UNP residues 39-302
Not recorded CL CHLORIDE ION × 5 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100 mM Tris pH 7.0 and 20% PEG 1000
Resolution 1.70 Å R-free 0.190
5SV3 RTA1-33/44-198 (RVEC) bound to Single Domain Antibody A3C8 Deposited 2016-08-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–233（198 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；0.1 M HEPES pH 7.0, 1.6 M Ammonium Sulfate
Resolution 2.73 Å R-free 0.267
5SV3 RTA1-33/44-198 (RVEC) bound to Single Domain Antibody A3C8 Deposited 2016-08-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 36–233（198 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；0.1 M HEPES pH 7.0, 1.6 M Ammonium Sulfate
Resolution 2.73 Å R-free 0.267
5U4L RTA-V1C7_G29R-high-salt Deposited 2016-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa） Fragment：residues 36-302
Not recorded PO4 PHOSPHATE ION × 3 CL CHLORIDE ION × 5 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；295 K；1.6 M ammonium dihydrogen phosphate, 20% glycerol, and 100 mM Tris pH 8.5
Resolution 2.50 Å R-free 0.257
5U4M RTA-V1C7-G29R-no_salt Deposited 2016-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–294（255 aa） Fragment：residues 40-294
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；295 K；8% PEG 4000 and 100 mM sodium acetate pH 4.6
Resolution 2.50 Å R-free 0.246
6CWG Ricin catalytic subunit bound go A9 VHH antibody Deposited 2018-03-30 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；295 K；200 mM Lithiuim sulfate, 100 mM CAPS pH 10.5, 2 M Ammonium sulfate
Resolution 2.60 Å R-free 0.262
6CWG Ricin catalytic subunit bound go A9 VHH antibody Deposited 2018-03-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 36–302（267 aa）
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；295 K；200 mM Lithiuim sulfate, 100 mM CAPS pH 10.5, 2 M Ammonium sulfate
Resolution 2.60 Å R-free 0.262
6OBC Ricin A chain bound to camelid Deposited 2019-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–298（259 aa） Fragment：Toxin catalytic subunit, residues 40-298
Not recorded CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；100 mM Tris (pH 7.0), 200 mM calcium acetate, and 20% PEG 3,000
Resolution 1.76 Å R-free 0.227
6OBE Ricin A chain bound to VHH antibody V6H8 Deposited 2019-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–302（265 aa） Fragment：Toxin catalytic subunit, residues 38-302
Not recorded NI NICKEL (II) ION × 2 EDO 1,2-ETHANEDIOL × 3 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；100 mM citric acid and 15% PEG
Resolution 1.73 Å R-free 0.208
6OBG Ricin A chain bound to VHH antibody V8E6 Deposited 2019-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–296（257 aa） Fragment：Toxin catalytic subunit, residues 40-296
Not recorded ZN ZINC ION × 5 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；295 K；100 mM MES (pH 6.0), 170 mM zinc acetate, 6% PEG 8,000, and 0.5% ethyl acetate
Resolution 2.00 Å R-free 0.218
6OBG Ricin A chain bound to VHH antibody V8E6 Deposited 2019-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–296（257 aa） Fragment：Toxin catalytic subunit, residues 40-296
Not recorded ZN ZINC ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；295 K；100 mM MES (pH 6.0), 170 mM zinc acetate, 6% PEG 8,000, and 0.5% ethyl acetate
Resolution 2.00 Å R-free 0.218
6OBM Ricin A chain bound to VHH antibody V6A7 Deposited 2019-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–298（259 aa） Fragment：Toxin catalytic subunit, residues 40-298
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；200 mM potassium sulfate and 20% PEG 3,350
Resolution 2.50 Å R-free 0.261
6OBO Ricin A chain bound to VHH antibody V6A6 Deposited 2019-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–296（257 aa） Fragment：Toxin catalytic subunit, residues 40-298
Not recorded EDO 1,2-ETHANEDIOL × 1 ACY ACETIC ACID × 3 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；100 mM imidazole (pH 8.0), 200 mM calcium acetate, and 15% PEG 8,000
Resolution 1.90 Å R-free 0.244
6OBO Ricin A chain bound to VHH antibody V6A6 Deposited 2019-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–296（257 aa） Fragment：Toxin catalytic subunit, residues 40-298
Not recorded EDO 1,2-ETHANEDIOL × 2 ACY ACETIC ACID × 3 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；100 mM imidazole (pH 8.0), 200 mM calcium acetate, and 15% PEG 8,000
Resolution 1.90 Å R-free 0.244
6OCA Ricin A chain bound to VHH antibody V2G10 Deposited 2019-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–302（265 aa） Fragment：Toxin catalytic subunit, residues 38-302
Not recorded CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；295 K；100 mM MES (pH 5.0) and 20% PEG 6,000
Resolution 2.11 Å R-free 0.246
6OCA Ricin A chain bound to VHH antibody V2G10 Deposited 2019-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 38–302（265 aa） Fragment：Toxin catalytic subunit, residues 38-302
Not recorded CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；295 K；100 mM MES (pH 5.0) and 20% PEG 6,000
Resolution 2.11 Å R-free 0.246
6OCD Ricin A chain bound to VHH antibody V6D4 Deposited 2019-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 40–297（258 aa） Fragment：Toxin catalytic subunit, residues 40-297
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；295 K；100 mM MES (pH 6.0), 400 mM zinc acetate, and 11% PEG 8,000
Resolution 2.10 Å R-free 0.228
6OCD Ricin A chain bound to VHH antibody V6D4 Deposited 2019-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 40–297（258 aa） Fragment：Toxin catalytic subunit, residues 40-297
Not recorded ZN ZINC ION × 2 IMD IMIDAZOLE × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；295 K；100 mM MES (pH 6.0), 400 mM zinc acetate, and 11% PEG 8,000
Resolution 2.10 Å R-free 0.228
6URW Crystal structure of ricin A chain in complex with inhibitor 4-(2-thienylmethyl)benzoic acid Deposited 2019-10-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded EDO 1,2-ETHANEDIOL × 22 DMS DIMETHYL SULFOXIDE × 1 R7T 4-[(thiophen-2-yl)methyl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Sodium Acetate, 20% (w/v) PEG 3350
Resolution 2.40 Å R-free 0.235
6URX Crystal structure of ricin A chain in complex with inhibitor 5-phenyl-2-thiophenecarboxylic acid Deposited 2019-10-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded EDO 1,2-ETHANEDIOL × 15 JMG 5-phenylthiophene-2-carboxylic acid × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Ammonium Iodide, 20% (w/v) PEG 3350
Resolution 1.99 Å R-free 0.218
6URY Crystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide Deposited 2019-10-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded R6T 9-oxo-9H-fluorene-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 17 CL CHLORIDE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；100 mM Tris pH 7.0, 200 mM Magnesium Chloride, 2.5 M Sodium Chloride
Resolution 1.54 Å R-free 0.195
6URY Crystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide Deposited 2019-10-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–302（267 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；100 mM Tris pH 7.0, 200 mM Magnesium Chloride, 2.5 M Sodium Chloride
Resolution 1.54 Å R-free 0.195
7KBI Ricin bound to VHH antibody V5E1 Deposited 2020-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；340 mM ammonium fluoride and 22% PEG 3,350.
Resolution 3.05 Å R-free 0.274
7KBK Ricin bound to VHH antibody V6E11 Deposited 2020-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；200 mM sodium chloride 100 mM CHES pH 9.5, and 1.26 M ammonium sulfate.
Resolution 2.09 Å R-free 0.203
7KC9 Ricin bound to VHH antibody V5G1 Deposited 2020-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded ZN ZINC ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；200 mM zinc acetate, 20% PEG 3,350
Resolution 2.30 Å R-free 0.238
7KC9 Ricin bound to VHH antibody V5G1 Deposited 2020-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 36–302（267 aa）
Chain E 315–576（262 aa）
Not recorded ZN ZINC ION × 5 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；200 mM zinc acetate, 20% PEG 3,350
Resolution 2.30 Å R-free 0.238
7KD0 Ricin bound to VHH antibody V2C11 Deposited 2020-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded GAL beta-D-galactopyranose × 2 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM Zinc Acetate, 14% PEG 8,000, 22% Glycerol, 80 mM NaCaco pH 6.5, 3% D+Galactose
Resolution 2.77 Å R-free 0.255
7KD2 Ricin bound to VHH antibody V11B2 Deposited 2020-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded ZN ZINC ION × 5 CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；200 mM Zinc Acetate, 100 mM MES pH 6.0, 10% PEG 8,000
Resolution 2.55 Å R-free 0.280
7KDM Ricin bound to VHH antibody V5G6 Deposited 2020-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 315–576（262 aa）
Not recorded ZN ZINC ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；4 M Sodium Formate
Resolution 2.30 Å R-free 0.238
7KDM Ricin bound to VHH antibody V5G6 Deposited 2020-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 315–576（262 aa）
Not recorded ZN ZINC ION × 5 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；4 M Sodium Formate
Resolution 2.30 Å R-free 0.238
7KDU Ricin bound to VHH antibody V5E4 Deposited 2020-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–302（267 aa）
Chain B 315–576（262 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；290 mM zinc Aaetate and 17% PEG 3,350
Resolution 2.81 Å R-free 0.294
7MLN Crystal structure of ricin A chain in complex with 5-(o-tolyl)thiophene-2-carboxylic acid Deposited 2021-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded ZJA 5-(2-methylphenyl)thiophene-2-carboxylic acid × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；24 %(w/v) PEG 1500, 20 %(w/v) Glycerol
Resolution 1.52 Å R-free 0.207
7MLO Crystal structure of ricin A chain in complex with 5-mesitylthiophene-2-carboxylic acid Deposited 2021-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded ZJ7 5-(2,4,6-trimethylphenyl)thiophene-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；50 mM Bis-Tris pH 6.5, 50 mM Ammonium Sulfate, 30 %(v/v) Pentaerythritol Ethoxylate (15/4 EO/OH)
Resolution 1.65 Å R-free 0.237
7MLO Crystal structure of ricin A chain in complex with 5-mesitylthiophene-2-carboxylic acid Deposited 2021-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–302（267 aa）
Not recorded ZJ7 5-(2,4,6-trimethylphenyl)thiophene-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；50 mM Bis-Tris pH 6.5, 50 mM Ammonium Sulfate, 30 %(v/v) Pentaerythritol Ethoxylate (15/4 EO/OH)
Resolution 1.65 Å R-free 0.237
7MLP Crystal structure of ricin A chain in complex with 5-(2,6-dimethylphenyl)thiophene-2-carboxylic acid Deposited 2021-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded ZJ4 5-(2,6-dimethylphenyl)thiophene-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；100 mM Sodium Acetate pH 4.5, 200 mM Zinc Acetate, 10 %(w/v) PEG 3000
Resolution 1.78 Å R-free 0.213
7MLT Crystal structure of ricin A chain in complex with 5-(2-ethylphenyl)thiophene-2-carboxylic acid Deposited 2021-04-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 18 ZJD 5-(2-ethylphenyl)thiophene-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；100 mM Tris pH 8.5, 200 mM Magnesium Chloride, 16 %(w/v) PEG 4000
Resolution 1.80 Å R-free 0.203
7TGF Single-domain VHH intrabodies neutralize ricin toxin. Deposited 2022-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；298 K；100 mM sodium citrate pH 4.0, 30% PEG 6000, and 1 M lithium chloride
Resolution 1.35 Å R-free 0.181
7TGI Single-domain VHH intrabodies neutralize ricin toxin Deposited 2022-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Not recorded CL CHLORIDE ION × 5 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；200 mM magnesium chloride, 20% PEG 3350
Resolution 2.10 Å R-free 0.222
7TH2 Single-domain VHH intrabodies neutralize ricin toxin Deposited 2022-01-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Not recorded CL CHLORIDE ION × 11 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM MES pH 6.5, 200 mM sodium thiocyanate, 8% dioxane, 1740 mM ammonium sulfate
Resolution 1.84 Å R-free 0.187
7TH2 Single-domain VHH intrabodies neutralize ricin toxin Deposited 2022-01-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–302（267 aa）
Not recorded CL CHLORIDE ION × 10 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM MES pH 6.5, 200 mM sodium thiocyanate, 8% dioxane, 1740 mM ammonium sulfate
Resolution 1.84 Å R-free 0.187
7XZS Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-L-tyrosine Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded I8T (2S)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-(4-hydroxyphenyl)propanoic acid × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, lithium sulfate, sodium acetate
Resolution 1.50 Å R-free 0.243
7XZT Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-D-tyrosine Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded I9P (2R)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-(4-hydroxyphenyl)propanoic acid × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.30 Å R-free 0.240
7XZU Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-L-phenylalanine Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IEK (2S)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-phenyl-propanoic acid × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.60 Å R-free 0.220
7XZW Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-D-phenylalanine Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IEW (2R)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-phenyl-propanoic acid × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.45 Å R-free 0.244
7Y02 Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-3-(4-fluorophenyl)propanoic acid Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IEZ (2S)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-(4-fluorophenyl)propanoic acid × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.60 Å R-free 0.223
7Y03 Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-2-phenylacetic acid Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IF4 (2S)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-2-phenyl-ethanoic acid × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.35 Å R-free 0.238
7Y05 Crystal structure of Ricin A chain bound with (R)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-2-phenylacetic acid Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IFH (2R)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-2-phenyl-ethanoic acid × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.60 Å R-free 0.231
7Y06 Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-4-phenylbutanoic acid Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IFQ (2S)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-4-phenyl-butanoic acid × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.35 Å R-free 0.235
7Y07 Crystal structure of Ricin A chain bound with (S)-2-amino-N-(1-hydroxy-3-phenylpropan-2-yl)-4-oxo-3,4-dihydropteridine-7-carboxamide Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IFX 2-azanyl-4-oxidanylidene-N-[(2S)-1-oxidanyl-3-phenyl-propan-2-yl]-3H-pteridine-7-carboxamide × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.25 Å R-free 0.234
7Y08 Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanine Deposited 2022-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded RS8 N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；Ammonium sulfate, Sodium malonate
Resolution 1.25 Å R-free 0.253
7Y4K Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-ornitine Deposited 2022-06-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded JKU (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-5-(phenylmethoxycarbonylamino)pentanoic acid × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.70 Å R-free 0.230
7Y4M Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-lysine Deposited 2022-06-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded IWQ (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-6-(phenylmethoxycarbonylamino)hexanoic acid × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG 2000, Lithium sulfate, Sodium acetate
Resolution 1.45 Å R-free 0.242
8I7P Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-tyrosine Deposited 2023-02-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–302（267 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；296 K；PEG2000, Lithium sulfate, Sodium acetate
Resolution 1.60 Å R-free 0.232
8T9V RTA-RUNT-59 complex structure Deposited 2023-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–296（258 aa）
Not recorded ZJT (9aP)-7-fluoro-4,5-dihydronaphtho[1,2-b]thiophene-2-carboxylic acid × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；200 mM di-Ammonium tartrate and 20% PEG 3350
Resolution 1.95 Å R-free 0.206
8TAB RTA-PD00589 Deposited 2023-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–296（258 aa）
Not recorded CL CHLORIDE ION × 3 U4T 4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 2 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；200 mM Mg(NO3)2 and 20% PEG 3350
Resolution 2.26 Å R-free 0.219
8TAD RTA in complex with inhibitor RUNT-206 Deposited 2023-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–293（255 aa）
Not recorded ZXJ (9aM)-5,5-dimethyl-4,5-dihydronaphtho[1,2-b]thiophene-2-carboxylic acid × 1 CL CHLORIDE ION × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；50 mM KH2PO4 and 20% PEG 8000
Resolution 2.76 Å R-free 0.256
8TFH Ricin in complex with Fab JB4 Deposited 2023-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 39–298（260 aa）
Chain B 315–576（262 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；1.5 M ammonium sulfate and 25% glycerol
Resolution 3.29 Å R-free 0.334
8TFL Ricin in complex with Fab SylH3 Deposited 2023-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 40–299（260 aa）
Chain B 316–576（261 aa）
Not recorded 2PE NONAETHYLENE GLYCOL × 1 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；1.5 M ammonium fluoride and 20% PEG 3,350
Resolution 2.89 Å R-free 0.287
9E3T RTA-RUNT-165 complex Deposited 2024-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa） Fragment：residues 40-294
Not recorded A1BH4 (5M)-5-(2-ethyl-6-methylphenyl)thiophene-2-carboxylic acid × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Hepes pH 6.5 and 20% PEG 6000
Resolution 1.80 Å R-free 0.234
9E3T RTA-RUNT-165 complex Deposited 2024-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–302（267 aa） Fragment：residues 40-294
Not recorded A1BH4 (5M)-5-(2-ethyl-6-methylphenyl)thiophene-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Hepes pH 6.5 and 20% PEG 6000
Resolution 1.80 Å R-free 0.234
9E40 RTA-RUNT-202 complex Deposited 2024-10-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa）
Not recorded A1BH3 5-(4-fluoro-2,6-dimethylphenyl)thiophene-2-carboxylic acid × 1 IMD IMIDAZOLE × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 NI NICKEL (II) ION × 4 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；Tris pH 7.0, 40% PEG 300, and 5% PEG 1000
Resolution 1.80 Å R-free 0.180
9E42 RTA-RUNT-192 complex Deposited 2024-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–302（267 aa） Fragment：residues 40-294
Not recorded A1BH2 5-(2,6-diethylphenyl)thiophene-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；170 mM diammonium hydrogen phosphate
Resolution 1.80 Å R-free 0.246
9E42 RTA-RUNT-192 complex Deposited 2024-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–302（267 aa） Fragment：residues 40-294
Not recorded A1BH2 5-(2,6-diethylphenyl)thiophene-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；170 mM diammonium hydrogen phosphate
Resolution 1.80 Å R-free 0.246

100 other PDB entries and 126 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RICI_RICCO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–267； UniProt 36–302

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7th3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7th3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7th3
Deposition date deposition_date2022-01-10
Structure title titleSingle-domain VHH intrabodies neutralize ricin toxin
Keywords keywordsAntibody-antigen complex, IMMUNE SYSTEM, IMMUNE SYSTEM-TOXIN complex; IMMUNE SYSTEM/TOXIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.61 Å
Radius of gyration Rg (electron density) rg_electron22.54 Å
Forward intensity I(0) i029929200.00
Molecular weight molecular_weight41500.0 kDa
Excluded volume excluded_volume51734 ų
Envelope volume envelope_volume61896 ų
Hydration-shell volume shell_volume23313 ų
Envelope diameter envelope_diameter81.1 Å
Shell Rg shell_rg28.94 Å
Envelope Rg envelope_rg22.70 Å
Shape Rg shape_rg22.54 Å
Total Rg total_rg23.34 Å
Total atoms total_atoms2928
Residues n_residues374
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.0 Å
Rg (real space) rg_real23.60 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real2.9930e+07
I(0) uncertainty (real space) i0_real_error3.6730e+05
Rg (reciprocal space) rg_reciprocal23.60 Å
I(0) (reciprocal space) i0_reciprocal29930000.0000
Solution quality estimate total_estimate0.8940
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.8 Å
Skewness Skewness skewness0.328
Kurtosis Kurtosis kurtosis-0.378
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha7471000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7th3B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)