Research workbench
Co-dehydrogenase homodimer from clostridium autoethanogenum at 1.90-a resolution
Analyse Co-dehydrogenase homodimer from clostridium autoethanogenum at 1.90-a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YU9
- Type
- protein
- Length
- 2,512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon-monoxide dehydrogenase (ACCEPTOR),CARBON-monoxide dehydrogenase (acceptor)
- EC
- 1.2.99.2
- UniProt
- U5RTE2
- Ligands
- SF4, XCC, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon-monoxide dehydrogenase (ACCEPTOR),CARBON-monoxide dehydrogenase (acceptor) (EC 1.2.99.2) | protein | 630 | 52% helix, 12% strand | U5RTE2 |
| B, D | Carbon-monoxide dehydrogenase (ACCEPTOR),CARBON-monoxide dehydrogenase (acceptor) (EC 1.2.99.2) | protein | 628 | 52% helix, 11% strand | U5RTE2 |
| C | Carbon-monoxide dehydrogenase (ACCEPTOR),CARBON-monoxide dehydrogenase (acceptor) (EC 1.2.99.2) | protein | 626 | 52% helix, 12% strand | U5RTE2 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, D
- XCC · FE(4)-NI(1)-S(4) cluster · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
- ACT · Acetate ion · additive · 5 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.80 | 0.93 | 65 | XCC |
| 2 | 193 | 0.80 | 0.94 | 59 | XCC |
| 3 | 214 | 0.79 | 0.92 | 64 | XCC |
| 4 | 252 | 0.78 | 0.91 | 43 | empty |
| 5 | 155 | 0.77 | 0.93 | 46 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3727 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 3711 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 203 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 197 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YU9 · CO-dehydrogenase homodimer from Clostridium autoethanogenum at 1.90-A resolution · 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 U5RTE2
- Elsewhere: RCSB PDB 6YU9 · PDBe 6YU9 · UniProt U5RTE2
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