MolNFT v1 · #171128 · protein
Co-dehydrogenase coupled to the N-terminal domain of the acetyl-CoA synthase from clostridium autoethanogenum isolated after tryptic digestion.
6YUA · Co DEHYDROGENASE/ACETYL-CoA synthase complex, beta subunit: “Co-dehydrogenase coupled to the N-terminal domain of the acetyl-CoA synthase from clostridium autoethanogenum…”. X-ray diffraction, 3 ligands (SF4, XCC, MG), 13 pockets…
- PDB
- 6YUA
- Type
- protein
- Length
- 1,848 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, 1.2.7.4
- UniProt
- U5RWA4, U5RTE2
- Ligands
- SF4, XCC, MG
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Co DEHYDROGENASE/ACETYL-CoA synthase complex, beta subunit (EC 2.3.1.169) | protein | 290 | 53% helix, 11% strand | U5RWA4 |
| B, C | Carbon-monoxide dehydrogenase (ACCEPTOR),CO-dehydrogenase from clostridium autoethanogenum dsm 10061 (EC 1.2.99.2, 1.2.7.4) | protein | 629 | 51% helix, 12% strand | U5RTE2 |
| D | Co DEHYDROGENASE/ACETYL-CoA synthase complex, beta subunit (EC 2.3.1.169) | protein | 300 | 52% helix, 10% strand | U5RWA4 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B, C
- XCC · FE(4)-NI(1)-S(4) cluster · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains C, B
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.87 | 0.88 | 172 | XCC, EDO |
| 2 | 988 | 0.87 | 0.88 | 185 | XCC |
| 3 | 217 | 0.79 | 0.93 | 44 | empty |
| 4 | 99 | 0.67 | 0.91 | 18 | SF4 |
| 5 | 414 | 0.66 | 0.79 | 46 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3709 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 991 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 961 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6YUA · CO-dehydrogenase coupled to the N-terminal domain of the Acetyl-CoA synthase from… · the same entry in another collection · chain C against C, 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 6YUA · PDBe 6YUA · UniProt U5RWA4 · UniProt U5RTE2
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