MolNFT v1 · #171112 · protein
Co-DEHYDROGENASE/ACETYL-CoA synthase (CODH/ACS) from clostridium autoethanogenum at 3.0-a resolution
6YTT · Co DEHYDROGENASE/ACETYL-CoA synthase complex, beta subunit: “Co-DEHYDROGENASE/ACETYL-CoA synthase (CODH/ACS) from clostridium autoethanogenum at 3.0-a resolution”. X-ray diffraction, 5 ligands (SF4, XCC, NA), 20 pockets (best…
- PDB
- 6YTT
- Type
- protein
- Length
- 2,672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Co DEHYDROGENASE/ACETYL-CoA synthase complex, beta subunit; Carbon-monoxide dehydrogenase…
- EC
- 2.3.1.169, 1.2.99.2
- UniProt
- U5RWA4, U5RTE2
- Ligands
- SF4, XCC, NA, NI, F
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Co DEHYDROGENASE/ACETYL-CoA synthase complex, beta subunit (EC 2.3.1.169) | protein | 708 | 40% helix, 17% strand | U5RWA4 |
| B | Carbon-monoxide dehydrogenase (ACCEPTOR),CARBON-monoxide dehydrogenase (acceptor) (EC 1.2.99.2) | protein | 629 | 52% helix, 11% strand | U5RTE2 |
| C | Carbon-monoxide dehydrogenase (ACCEPTOR),CARBON-monoxide dehydrogenase (acceptor) (EC 1.2.99.2) | protein | 630 | 52% helix, 11% strand | U5RTE2 |
| D | Co DEHYDROGENASE/ACETYL-CoA synthase complex, beta subunit (EC 2.3.1.169) | protein | 705 | 40% helix, 17% strand | U5RWA4 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 5 copies · chains A, B, C, D
- XCC · FE(4)-NI(1)-S(4) cluster · ligand · 2 copies · chains B, C
- NA · Sodium ion · metal · 6 copies · chains B, C
- NI · Nickel (II) ion · metal · 4 copies · chains A, D
- F · Fluoride ion · ion · 9 copies · chains A, B, C
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.87 | 0.91 | 140 | XCC |
| 2 | 800 | 0.84 | 0.86 | 150 | GOL |
| 3 | 1167 | 0.80 | 0.81 | 116 | empty |
| 4 | 217 | 0.78 | 0.92 | 46 | empty |
| 5 | 84 | 0.77 | 0.98 | 21 | XCC |
Interfaces
3 interfaces between chains.
- B–C · 3733 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 1143 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 949 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6YTT · CO-dehydrogenase/Acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum at 3.0-A… · 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 U5RWA4
- Every structure of UniProt U5RTE2
- Elsewhere: RCSB PDB 6YTT · PDBe 6YTT · UniProt U5RWA4 · UniProt U5RTE2
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