MolNFT v1 · #143686 · protein
Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 2), oxidized C-cluster
6B6W: “Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 2)…”. X-ray diffraction, 6 ligands (SF4, XCC, CUV), 10 pockets (best druggability 0.80). MolNFT v1 #143686 on GenesisL1: 3D…
- PDB
- 6B6W
- Type
- protein
- Length
- 1,254 residues
- Chains
- 2
- 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, CUV, FES, MG, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 626 | 53% helix, 11% strand | Q72A99 |
| B | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 628 | 53% helix, 11% strand | Q72A99 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- XCC · FE(4)-NI(1)-S(4) cluster · ligand · 2 copies · chains A, B
- CUV · Fe(4)-Ni(1)-S(4) cluster, oxidized · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.80 | 0.98 | 31 | empty |
| 2 | 286 | 0.59 | 0.78 | 43 | MG |
| 3 | 311 | 0.58 | 0.77 | 43 | MG, GOL |
| 4 | 96 | 0.43 | 0.78 | 22 | empty |
| 5 | 57 | 0.39 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3971 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6B6W · Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated… · 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 6B6W · PDBe 6B6W · UniProt Q72A99
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