Research workbench
Xenon-bound structure of carbon monoxide dehydrogenase (codh) from desulfovibrio vulgaris
Analyse Xenon-bound structure of carbon monoxide dehydrogenase (codh) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TSJ
- Type
- protein
- Length
- 621 residues
- Chains
- 1
- 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, FES, CUV, XE
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 621 | 52% helix, 11% strand | Q72A99 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- CUV · Fe(4)-Ni(1)-S(4) cluster, oxidized · ligand · chains A
- XE · Xenon · ion · 12 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.78 | 0.93 | 50 | XE |
| 2 | 60 | 0.71 | 0.97 | 24 | CUV |
| 3 | 78 | 0.66 | 0.92 | 27 | XE |
| 4 | 75 | 0.51 | 0.85 | 17 | empty |
| 5 | 223 | 0.47 | 0.74 | 27 | empty |
Compared structures
- 7TSJ · Xenon-bound structure of carbon monoxide dehydrogenase (CODH) from Desulfovibrio vulgaris · 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 7TSJ · PDBe 7TSJ · UniProt Q72A99
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