RICIN A CHAIN
Ricinus communis
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 36–302 | 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 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 36–302 | Not recorded | No other associated polymer | 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 |
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 1IL5 | 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 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 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 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 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 |
| 1IL9 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 8-METHYL-9-OXOGUANINE Deposited 2001-05-07 | 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 |
| 7TH3 Single-domain VHH intrabodies neutralize ricin toxin Deposited 2022-01-10 | Different oligomeric state 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 7.5；298 K；418 mM ammonium chloride, 22% PEG 3350
|
Resolution 2.29 Å R-free 0.272 |
| 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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 125 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 Author chain B； PDBConstruct 1–267； UniProt 36–302 |
