MolNFT v1 · #173731 · protein
Coos-V with xe-soaked
7B9A · Carbon monoxide dehydrogenase: “Coos-V with xe-soaked”. X-ray diffraction, 6 ligands (SF4, T2N, FES), 20 pockets (best druggability 0.81). MolNFT v1 #173731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7B9A
- Type
- protein
- Length
- 2,515 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
- Q3AG28
- Ligands
- SF4, T2N, FES, XE, BR, H2S
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 629 | 53% helix, 12% strand | Q3AG28 |
| B | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 628 | 52% helix, 12% strand | Q3AG28 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- 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 · 4 copies · chains A, B, C, D
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B, C, D
- XE · Xenon · ion · 61 copies · chains A, B, C, D
- BR · Bromide ion · ion · 23 copies · chains A, B, C, D
- H2S · Hydrosulfuric acid · ion · 3 copies · chains A, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.81 | 0.96 | 48 | XE |
| 2 | 128 | 0.79 | 0.97 | 45 | XE |
| 3 | 115 | 0.76 | 0.94 | 38 | XE |
| 4 | 364 | 0.74 | 0.84 | 66 | XE |
| 5 | 84 | 0.74 | 0.96 | 29 | XE |
Interfaces
4 interfaces between chains.
- C–D · 3992 Ų buried · 74 hydrogen bonds · protein-protein
- A–B · 3982 Ų buried · 78 hydrogen bonds · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7B9A · CooS-V with Xe-soaked · 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 7B9A · PDBe 7B9A · UniProt Q3AG28
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