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Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase, dithionite-reduced then oxygen-exposed (protein batch 2), oxidized 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
- 6B6Y
- Type
- protein
- Length
- 1,233 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, CUV, FES
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 616 | 51% helix, 11% strand | Q72A99 |
| B | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 617 | 52% helix, 11% strand | Q72A99 |
Ligands and binding sites
- SF4 · Iron/sulfur 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
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.84 | 0.96 | 39 | empty |
| 2 | 59 | 0.64 | 0.93 | 23 | empty |
| 3 | 297 | 0.57 | 0.77 | 44 | empty |
| 4 | 307 | 0.56 | 0.76 | 43 | empty |
| 5 | 102 | 0.45 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3666 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 6B6Y · Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase… · 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 6B6Y · PDBe 6B6Y · UniProt Q72A99
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