Research workbench
Crystal structure of carbon monoxide dehydrogenase from rhodospirillum rubrum
Analyse Crystal structure of carbon monoxide dehydrogenase from rhodospirillum rubrum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JQK
- Type
- protein
- Length
- 3,660 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide dehydrogenase
- EC
- 1.2.99.2
- UniProt
- P31896
- Ligands
- SF4, WCC, FE2, UNX
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Carbon monoxide dehydrogenase (EC 1.2.99.2) | protein | 610 | 50% helix, 12% strand | P31896 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, D, E, F
- WCC · FE(3)-NI(1)-S(4) cluster · ligand · 6 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- UNX · Unknown atom or ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.84 | 0.86 | 106 | SF4 |
| 2 | 182 | 0.83 | 0.97 | 23 | empty |
| 3 | 176 | 0.79 | 0.94 | 53 | empty |
| 4 | 239 | 0.79 | 0.91 | 69 | empty |
| 5 | 152 | 0.78 | 0.94 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3991 Ų buried · 82 hydrogen bonds · protein-protein
- C–D · 3958 Ų buried · 76 hydrogen bonds · protein-protein
- E–F · 3950 Ų buried · 77 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 512 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1JQK · Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum · the same entry in another collection · chain F against F, TM-score 1.00
- P31896 · AlphaFold monomer V2.0 prediction for carbon monoxide dehydrogenase (P31896) · a predicted model of the same protein · chain E 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 P31896
- Elsewhere: RCSB PDB 1JQK · PDBe 1JQK · UniProt P31896
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