MolNFT v1 · #15475 · protein
Crystal structure of the CU,MO-co dehydrogenase (codh); oxidized form
1N5W · Carbon monoxide dehydrogenase small chain: “Crystal structure of the CU,MO-co dehydrogenase (codh); oxidized form”. X-ray diffraction, 5 ligands (FES, CUM, MCN), 20 pockets (best druggability 0.87). MolNFT v1 #15475 on GenesisL1: 3D…
- PDB
- 1N5W
- Type
- protein
- Length
- 2,491 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide dehydrogenase small chain; Carbon monoxide dehydrogenase large chain…
- EC
- 1.2.99.2
- UniProt
- P19921, P19919, P19920
- Ligands
- FES, CUM, MCN, FAD, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon monoxide dehydrogenase small chain (EC 1.2.99.2) | protein | 161 | 39% helix, 17% strand | P19921 |
| B | Carbon monoxide dehydrogenase large chain (EC 1.2.99.2) | protein | 804 | 31% helix, 26% strand | P19919 |
| C | Carbon monoxide dehydrogenase medium chain (EC 1.2.99.2) | protein | 287 | 37% helix, 27% strand | P19920 |
| D | Carbon monoxide dehydrogenase small chain (EC 1.2.99.2) | protein | 158 | 40% helix, 17% strand | P19921 |
| E | Carbon monoxide dehydrogenase large chain (EC 1.2.99.2) | protein | 795 | 30% helix, 26% strand | P19919 |
| F | Carbon monoxide dehydrogenase medium chain (EC 1.2.99.2) | protein | 286 | 37% helix, 27% strand | P19920 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B, D, E
- CUM · Cu(i)-S-mo(vi)(=o)oh cluster · ligand · 2 copies · chains B, E
- MCN · Pterin cytosine dinucleotide · ligand · 2 copies · chains A, B, D, E
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C, D, F
- PO4 · Phosphate ion · ion · chains A
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 | 374 | 0.87 | 0.96 | 76 | CUM, MCN |
| 2 | 242 | 0.84 | 0.97 | 45 | CUM, MCN |
| 3 | 1128 | 0.82 | 0.83 | 122 | FAD |
| 4 | 1106 | 0.81 | 0.82 | 129 | FAD |
| 5 | 895 | 0.78 | 0.81 | 80 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2328 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2305 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 2122 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1317 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 1273 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1N5W · Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Oxidized form · the same entry in another collection · chain F against F, TM-score 1.00
- P19920 · AlphaFold monomer V2.0 prediction for carbon monoxide dehydrogenase medium chain (P19920) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P19919 · AlphaFold monomer V2.0 prediction for carbon monoxide dehydrogenase large chain (P19919) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P19921 · AlphaFold monomer V2.0 prediction for carbon monoxide dehydrogenase small chain (P19921) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P19921
- Every structure of UniProt P19919
- Every structure of UniProt P19920
- Elsewhere: RCSB PDB 1N5W · PDBe 1N5W · UniProt P19921 · UniProt P19919 · UniProt P19920
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