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Native structure of bifunctional carbon monoxide DEHYDROGENASE/ACETYL- CoA synthase from moorella thermoacetica, water-bound C-cluster.
Analyse Native structure of bifunctional carbon monoxide DEHYDROGENASE/ACETYL- CoA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I01
- Type
- protein
- Length
- 5,604 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit beta; Carbon monoxide…
- EC
- 1.2.7.4, 1.2.99.2, 2.3.1.169
- UniProt
- P27989, P27988
- Ligands
- SF4, XCC, CU1, NI, NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit beta (EC 1.2.7.4, 1.2.99.2) | protein | 673 | 51% helix, 11% strand | P27989 |
| M, N, O, P | Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit alpha (EC 2.3.1.169) | protein | 728 | 43% helix, 17% strand | P27988 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, B, C, D, M, N, O, P
- XCC · FE(4)-NI(1)-S(4) cluster · ligand · 4 copies · chains A, B, C, D
- CU1 · Copper (I) ion · metal · 4 copies · chains M, N, O, P
- NI · Nickel (II) ion · metal · 4 copies · chains M, N, O, P
- NA · Sodium ion · metal · 4 copies · chains M, N, O, P
- GOL · Glycerol · additive · 4 copies · chains A, M, B, N, C, O, D, P
- ACT · Acetate ion · additive · 4 copies · chains M, N, O, P
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 | 192 | 0.85 | 0.98 | 65 | empty |
| 2 | 126 | 0.81 | 0.98 | 52 | empty |
| 3 | 121 | 0.81 | 0.98 | 49 | empty |
| 4 | 122 | 0.80 | 0.98 | 51 | empty |
| 5 | 567 | 0.78 | 0.84 | 74 | empty |
Interfaces
12 interfaces between chains.
- C–D · 4113 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 4091 Ų buried · 68 hydrogen bonds · protein-protein
- A–M · 1940 Ų buried · 19 hydrogen bonds · protein-protein
- B–N · 1900 Ų buried · 24 hydrogen bonds · protein-protein
- D–P · 1871 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3I01 · Native structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from… · the same entry in another collection · chain P against P, TM-score 1.00
- P27989 · AlphaFold monomer V2.0 prediction for carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase… · a predicted model of the same protein · chain B 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 P27989
- Every structure of UniProt P27988
- Elsewhere: RCSB PDB 3I01 · PDBe 3I01 · UniProt P27989 · UniProt P27988
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