Research workbench
Structure of ricin a chain bound with N-(N-(pterin-7-YL)CARBONYL-L- serinyl)-L-tryptophan
Analyse Structure of ricin a chain bound with N-(N-(pterin-7-YL)CARBONYL-L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HV3
- Type
- protein
- Length
- 268 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- 19L, SO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (EC 3.2.2.22) | protein | 268 | 40% helix, 21% strand | P02879 |
Ligands and binding sites
- 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 · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- MLA · Malonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.60 | 0.80 | 38 | 19L |
| 2 | 130 | 0.46 | 0.77 | 17 | empty |
| 3 | 68 | 0.43 | 0.81 | 13 | MLA |
| 4 | 66 | 0.33 | 0.76 | 16 | empty |
Compared structures
- 4HV3 · Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonyl-L-serinyl)-L-tryptophan · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P02879
- Elsewhere: RCSB PDB 4HV3 · PDBe 4HV3 · UniProt P02879
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