MolNFT v1 · #107560 · protein
CO2 bound to cluster C of NI,FE-co dehydrogenase at true-atomic resolution
4UDX · Carbon monoxide dehydrogenase 2: “CO2 bound to cluster C of NI,FE-co dehydrogenase at true-atomic resolution”. X-ray diffraction, 5 ligands (SF4, FES, WCC), 5 pockets (best druggability 0.58). MolNFT v1 #107560 on GenesisL1: 3D…
- PDB
- 4UDX
- Type
- protein
- Length
- 633 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide dehydrogenase 2
- EC
- 1.2.99.2
- UniProt
- Q9F8A8
- Ligands
- SF4, FES, WCC, FE2, CO2
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Carbon monoxide dehydrogenase 2 (EC 1.2.99.2) | protein | 633 | 53% helix, 11% strand | Q9F8A8 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains X
- FES · Fe2/s2 (inorganic) cluster · ligand · chains X
- WCC · FE(3)-NI(1)-S(4) cluster · ligand · chains X
- FE2 · Fe (II) ion · metal · chains X
- CO2 · Carbon dioxide · ion · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.58 | 0.75 | 51 | empty |
| 2 | 51 | 0.57 | 0.90 | 14 | empty |
| 3 | 163 | 0.46 | 0.76 | 24 | empty |
| 4 | 62 | 0.26 | 0.72 | 20 | empty |
| 5 | 50 | 0.23 | 0.72 | 17 | empty |
Compared structures
- 4UDX · CO2 bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic resolution · the same entry in another collection · chain X against X, TM-score 1.00
- Q9F8A8 · AlphaFold monomer V2.0 prediction for carbon monoxide dehydrogenase 2 (Q9F8A8) · a predicted model of the same protein · chain X 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 Q9F8A8
- Elsewhere: RCSB PDB 4UDX · PDBe 4UDX · UniProt Q9F8A8
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