MolNFT v1 · #56237 · protein
Xenon-bound structure of bifunctional carbon monoxide DEHYDROGENASE/ACETYL-CoA SYNTHASE(CODH/ACS) from moorella thermoacetica
2Z8Y · Carbon monoxide DEHYDROGENASE/ACETYL CoA synthase subunit…: “Xenon-bound structure of bifunctional carbon monoxide DEHYDROGENASE/ACETYL-CoA SYNTHASE(CODH/ACS) from…”. X-ray diffraction, 5 ligands (SF4, XCC, CU1), 20 pockets (best…
- PDB
- 2Z8Y
- Type
- protein
- Length
- 5,603 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, XE
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 43% 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, 9% strand | P27989 |
| M, N, P | Carbon monoxide DEHYDROGENASE/ACETYL CoA synthase subunit alpha (EC 2.3.1.169) | protein | 728 | 43% helix, 16% strand | P27988 |
| O | Carbon monoxide DEHYDROGENASE/ACETYL CoA synthase subunit alpha (EC 2.3.1.169) | protein | 727 | 36% helix, 15% 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
- XE · Xenon · ion · 38 copies · chains A, M, B, N, C, O, D, P
- GOL · Glycerol · additive · 11 copies · chains A, M, B, N, C, D, 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 | 197 | 0.85 | 0.98 | 70 | XE |
| 2 | 176 | 0.84 | 0.98 | 64 | XE |
| 3 | 140 | 0.82 | 0.98 | 50 | XE |
| 4 | 151 | 0.82 | 0.98 | 51 | XE |
| 5 | 1031 | 0.81 | 0.83 | 100 | SF4 |
Interfaces
12 interfaces between chains.
- C–D · 4076 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 4022 Ų buried · 66 hydrogen bonds · protein-protein
- A–M · 1927 Ų buried · 19 hydrogen bonds · protein-protein
- B–N · 1906 Ų buried · 21 hydrogen bonds · protein-protein
- C–O · 1894 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2Z8Y · Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA… · 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 2Z8Y · PDBe 2Z8Y · UniProt P27989 · UniProt P27988
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