Research workbench
Reconstituted co dehydrogenase from oligotropha carboxidovorans
Analyse Reconstituted co dehydrogenase from oligotropha carboxidovorans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZXI
- 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, CU, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 34% 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 | 32% 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 | 39% helix, 17% strand | P19921 |
| E | Carbon monoxide dehydrogenase large chain (EC 1.2.99.2) | protein | 795 | 31% helix, 26% strand | P19919 |
| F | Carbon monoxide dehydrogenase medium chain (EC 1.2.99.2) | protein | 286 | 38% 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
- CU · Copper (II) ion · metal · 2 copies · chains B, E
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.88 | 0.95 | 88 | CU, CUM, MCN |
| 2 | 433 | 0.87 | 0.95 | 89 | CUM, MCN |
| 3 | 1089 | 0.81 | 0.82 | 127 | FAD |
| 4 | 1113 | 0.81 | 0.82 | 132 | FAD |
| 5 | 803 | 0.77 | 0.81 | 79 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2331 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2317 Ų buried · 36 hydrogen bonds · protein-protein
- B–E · 2139 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1313 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1290 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1ZXI · Reconstituted CO dehydrogenase from Oligotropha carboxidovorans · 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 1ZXI · PDBe 1ZXI · UniProt P19921 · UniProt P19919 · UniProt P19920
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