Research workbench
Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase C301S variant
Analyse Crystal structure of desulfovibrio vulgaris carbon monoxide dehydrogenase C301S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DC2
- Type
- protein
- Length
- 2,499 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
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 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 |
| C | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 623 | 53% helix, 12% strand | Q72A99 |
| D | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 626 | 54% 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 · 5 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, C, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.79 | 0.97 | 32 | empty |
| 2 | 125 | 0.79 | 0.97 | 31 | empty |
| 3 | 95 | 0.76 | 0.96 | 38 | empty |
| 4 | 64 | 0.73 | 0.98 | 27 | empty |
| 5 | 59 | 0.71 | 0.97 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3957 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 3956 Ų buried · 74 hydrogen bonds · protein-protein
- A–C · 145 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DC2 · Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase C301S variant · 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 6DC2 · PDBe 6DC2 · UniProt Q72A99
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.