MolNFT v1 · #173675 · protein
Coos-V with oxidized hybrid cluster
7B7Q · Carbon monoxide dehydrogenase: “Coos-V with oxidized hybrid cluster”. X-ray diffraction, 4 ligands (SF4, T2N, FES), 9 pockets (best druggability 0.79). MolNFT v1 #173675 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7B7Q
- Type
- protein
- Length
- 1,258 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
- Q3AG28
- Ligands
- SF4, T2N, FES, TAM
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 629 | 54% helix, 12% strand | Q3AG28 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- T2N · 3,5-dioxa-7-thia-1-thionia-2$L^{2},4$L^{2},6$L^{3}, 8$L^{2}-tetraferrabicyclo[4.2.0]octane · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.79 | 0.97 | 36 | empty |
| 2 | 125 | 0.76 | 0.94 | 40 | PEG |
| 3 | 105 | 0.74 | 0.95 | 33 | empty |
| 4 | 55 | 0.52 | 0.87 | 17 | empty |
| 5 | 124 | 0.48 | 0.80 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 4069 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7B7Q · CooS-V with oxidized hybrid cluster · 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 Q3AG28
- Elsewhere: RCSB PDB 7B7Q · PDBe 7B7Q · UniProt Q3AG28
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