Research workbench
Crystal structure of a truncated acetyl-CoA synthase
Analyse Crystal structure of a truncated acetyl-CoA synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GIT
- Type
- protein
- Length
- 2,528 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit alpha
- EC
- 2.3.1.169
- UniProt
- P27988
- Ligands
- SF4, ZN, SO4, H2S
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit alpha (EC 2.3.1.169) | protein | 422 | 36% helix, 21% strand | P27988 |
| B, C, E, F | Carbon monoxide DEHYDROGENASE/ACETYL-CoA synthase subunit alpha (EC 2.3.1.169) | protein | 421 | 37% helix, 21% strand | P27988 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 24 copies · chains A, E, F, B, C, D
- H2S · Hydrosulfuric acid · ion · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
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 | 925 | 0.88 | 0.90 | 152 | ZN, H2S, GOL |
| 2 | 808 | 0.88 | 0.91 | 131 | H2S |
| 3 | 1021 | 0.88 | 0.89 | 143 | H2S, GOL |
| 4 | 968 | 0.82 | 0.84 | 91 | H2S, GOL |
| 5 | 573 | 0.73 | 0.81 | 53 | empty |
Interfaces
12 interfaces between chains.
- A–C · 907 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 904 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 869 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 800 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 797 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3GIT · Crystal structure of a truncated acetyl-CoA synthase · the same entry in another collection · chain F against F, TM-score 1.00
- P27988 · 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 0.97
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 P27988
- Elsewhere: RCSB PDB 3GIT · PDBe 3GIT · UniProt P27988
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