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As-isolated ni-free crystal structure of carbon monoxide dehydrogenase from thermococcus sp. AM4 produced without cooc maturase
Analyse As-isolated ni-free crystal structure of carbon monoxide dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T7J
- Type
- protein
- Length
- 1,892 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide dehydrogenase
- EC
- 1.2.7.4
- UniProt
- B7R5K0
- Ligands
- SF4, FES, MSK, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 632 | 52% helix, 11% strand | B7R5K0 |
| A | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 631 | 52% helix, 10% strand | B7R5K0 |
| D | Carbon monoxide dehydrogenase (EC 1.2.7.4) | protein | 629 | 51% helix, 11% strand | B7R5K0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B, A, D
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains B, A, D
- MSK · Broken Fe4S4 cluster · ligand · 3 copies · chains B, A, D
- PO4 · Phosphate ion · ion · 4 copies · chains B, A, D
- BU3 · (R,R)-2,3-butanediol · additive · 3 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · chains B
- CIT · Citric acid · additive · chains B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.76 | 0.95 | 36 | empty |
| 2 | 95 | 0.75 | 0.95 | 26 | empty |
| 3 | 112 | 0.74 | 0.94 | 36 | empty |
| 4 | 1108 | 0.73 | 0.76 | 88 | PO4, BU3, CIT |
| 5 | 67 | 0.73 | 0.97 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–D · 314 Ų buried · 3 hydrogen bonds · protein-protein
- B–A · 276 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6T7J · As-isolated Ni-free crystal structure of carbon monoxide dehydrogenase from Thermococcus… · the same entry in another collection · chain B against B, 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 B7R5K0
- Elsewhere: RCSB PDB 6T7J · PDBe 6T7J · UniProt B7R5K0
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