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Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 1), canonical C-cluster
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
- 6B6V
- Type
- protein
- Length
- 1,250 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, FES
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 625 | 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
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.78 | 0.97 | 29 | empty |
| 2 | 89 | 0.77 | 0.98 | 34 | XCC |
| 3 | 115 | 0.74 | 0.94 | 34 | empty |
| 4 | 96 | 0.71 | 0.93 | 31 | empty |
| 5 | 335 | 0.61 | 0.78 | 42 | GOL |
Interfaces
1 interface between chains.
- A–B · 3905 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 6B6V · 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 6B6V · PDBe 6B6V · UniProt Q72A99
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