Research workbench
NIZN[FE4S4] and NINI[FE4S4] clusters in closed and open alpha subunits of acetyl-CoA SYNTHASE/CARBON monoxide dehydrogenase
Analyse NIZN[FE4S4] and NINI[FE4S4] clusters in closed and open alpha subunits of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OAO
- Type
- protein
- Length
- 2,803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit beta; Carbon monoxide…
- EC
- 1.2.99.2, 1.2.7.4, 2.3.1.169
- UniProt
- P27989, P27988
- Ligands
- SF4, XCC, FOR, BCT, SX, NI, FE2, ZN, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit beta (EC 1.2.99.2, 1.2.7.4) | protein | 673 | 51% helix, 11% strand | P27989 |
| C | Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit alpha (EC 2.3.1.169) | protein | 729 | 44% helix, 17% strand | P27988 |
| D | Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit alpha (EC 2.3.1.169) | protein | 728 | 44% helix, 17% strand | P27988 |
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 A, B
- FOR · Formyl group · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · chains B
- SX · Sulfur oxide · ligand · chains C
- NI · Nickel (II) ion · metal · 3 copies · chains C, D
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains C
- SO4 · Sulfate ion · ion · 31 copies · chains A, D, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.84 | 0.98 | 59 | empty |
| 2 | 945 | 0.78 | 0.80 | 71 | SF4, ACT |
| 3 | 86 | 0.78 | 0.98 | 35 | empty |
| 4 | 634 | 0.77 | 0.82 | 70 | SF4 |
| 5 | 446 | 0.76 | 0.85 | 55 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 4090 Ų buried · 80 hydrogen bonds · protein-protein
- B–C · 1873 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1823 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 596 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1OAO · NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA… · the same entry in another collection · chain D against D, 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 0.99
- P27988 · AlphaFold monomer V2.0 prediction for carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase… · a predicted model of the same protein · chain C against A, TM-score 0.77
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 1OAO · PDBe 1OAO · UniProt P27989 · UniProt P27988
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