Research workbench
Crystal structure of C45G/T50C D. vulgaris carbon monoxide dehydrogenase (anaerobic)
Analyse Crystal structure of C45G/T50C D. 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
- 6VWY
- Type
- protein
- Length
- 1,251 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
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 626 | 53% helix, 12% strand | Q72A99 |
| B | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 625 | 52% helix, 12% strand | Q72A99 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 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
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.83 | 0.98 | 32 | empty |
| 2 | 63 | 0.72 | 0.98 | 26 | empty |
| 3 | 58 | 0.69 | 0.95 | 23 | empty |
| 4 | 331 | 0.60 | 0.78 | 44 | empty |
| 5 | 322 | 0.59 | 0.78 | 43 | GOL |
Interfaces
1 interface between chains.
- A–B · 3867 Ų buried · 79 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VWY · Crystal structure of C45G/T50C D. vulgaris carbon monoxide dehydrogenase (anaerobic) · 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 6VWY · PDBe 6VWY · UniProt Q72A99
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