Research workbench
Monomeric acetyl-CoA synthase in closed conformation
Analyse Monomeric acetyl-CoA synthase in closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NYP
- Type
- protein
- Length
- 1,458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Co-methylating acetyl-CoA synthase
- EC
- 2.3.1.169
- UniProt
- Q3ACS4
- Ligands
- SF4, UW8, NI
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Co-methylating acetyl-CoA synthase (EC 2.3.1.169) | protein | 729 | 43% helix, 16% strand | Q3ACS4 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- UW8 · 2-[3,8,8,12,12-pentakis(2-hydroxy-2-oxoethyl)-2,7,11-tris(oxidanylidene)-1,4,6,9,10,13-hexaoxa-5$l^{6}-titanaspiro[4.4^{5}.4^{5}]tridecan-3-yl]ethanoic acid · ligand · 2 copies · chains B, A
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.76 | 0.80 | 69 | SF4 |
| 2 | 1053 | 0.76 | 0.78 | 82 | SF4 |
| 3 | 448 | 0.67 | 0.79 | 24 | empty |
| 4 | 343 | 0.62 | 0.78 | 35 | empty |
| 5 | 490 | 0.62 | 0.75 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7NYP · monomeric acetyl-CoA synthase in closed conformation · 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 Q3ACS4
- Elsewhere: RCSB PDB 7NYP · PDBe 7NYP · UniProt Q3ACS4
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