Research workbench
Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase produced without cooc, reduced
Analyse Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OND
- Type
- protein
- Length
- 2,505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide dehydrogenase
- EC
- 1.2.7.4
- UniProt
- Q72A99
- Ligands
- SF4, XCC, FES, MG, FE, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 626 | 53% helix, 11% strand | Q72A99 |
| D | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 627 | 53% helix, 11% strand | Q72A99 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- XCC · FE(4)-NI(1)-S(4) cluster · ligand · 4 copies · chains A, B, C, D
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.81 | 0.97 | 31 | empty |
| 2 | 147 | 0.80 | 0.97 | 30 | empty |
| 3 | 62 | 0.73 | 0.98 | 26 | empty |
| 4 | 59 | 0.72 | 0.98 | 26 | empty |
| 5 | 348 | 0.61 | 0.78 | 44 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3969 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 3965 Ų buried · 75 hydrogen bonds · protein-protein
- B–C · 65 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6OND · Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced… · 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 Q72A99
- Elsewhere: RCSB PDB 6OND · PDBe 6OND · UniProt Q72A99
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