MolNFT v1 · #137478 · protein
Crystal structure of apo cryptococcus neoformans H99 acetyl-CoA synthetase with an acetylated active site lysine
5VPV · Acetyl-coenzyme a synthetase: “Crystal structure of apo cryptococcus neoformans H99 acetyl-CoA synthetase with an acetylated active site…”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.88). MolNFT v1 #137478 on…
- PDB
- 5VPV
- Type
- protein
- Length
- 1,825 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-coenzyme a synthetase
- EC
- 6.2.1.1
- UniProt
- J9VFT1
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 657 | 33% helix, 22% strand | J9VFT1 |
| B | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 649 | 32% helix, 23% strand | J9VFT1 |
| C | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 519 | 31% helix, 22% strand | J9VFT1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.88 | 0.90 | 137 | empty |
| 2 | 615 | 0.67 | 0.76 | 59 | GOL, PO4 |
| 3 | 460 | 0.64 | 0.77 | 56 | PO4 |
| 4 | 375 | 0.58 | 0.75 | 53 | GOL, PO4 |
| 5 | 187 | 0.56 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 879 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 844 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 5VPV · Crystal structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Synthetase with an… · 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 J9VFT1
- Elsewhere: RCSB PDB 5VPV · PDBe 5VPV · UniProt J9VFT1
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