Research workbench
Crystal structure of ricin a chain in complex with inhibitor 9-oxo-4- fluorenecarboxamide
Analyse Crystal structure of ricin a chain in complex with inhibitor 9-oxo-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6URY
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- R6T, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (EC 3.2.2.22) | protein | 268 | 39% helix, 21% strand | P02879 |
| B | Ricin (EC 3.2.2.22) | protein | 260 | 40% helix, 22% strand | P02879 |
Ligands and binding sites
- R6T · 9-oxo-9H-fluorene-4-carboxamide · ligand · chains A
- CL · Chloride ion · ion · 16 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.77 | 0.79 | 89 | CL |
| 2 | 268 | 0.56 | 0.77 | 34 | EDO |
| 3 | 101 | 0.43 | 0.77 | 13 | empty |
| 4 | 56 | 0.36 | 0.78 | 13 | empty |
| 5 | 68 | 0.31 | 0.74 | 16 | EDO, CL |
Interfaces
1 interface between chains.
- A–B · 319 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6URY · Crystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide · the same entry in another collection · chain B against B, 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 6URY · PDBe 6URY · UniProt P02879
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