MolNFT v1 · #124209 · protein
Crystal structure of acetyl-CoA synthetase in complex with ATP and acetyl-AMP from cryptococcus neoformans H99
5K8F · Acetyl-coenzyme a synthetase: “Crystal structure of acetyl-CoA synthetase in complex with ATP and acetyl-AMP from cryptococcus neoformans H99”. X-ray diffraction, 4 ligands (ATP, 6R9, MG), 20 pockets (best druggability 0.89). MolNFT…
- PDB
- 5K8F
- Type
- protein
- Length
- 1,962 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
- ATP, 6R9, MG, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 656 | 31% helix, 22% strand | J9VFT1 |
| B | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 655 | 33% helix, 22% strand | J9VFT1 |
| C | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 651 | 33% helix, 23% strand | J9VFT1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- 6R9 · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.89 | 0.90 | 130 | empty |
| 2 | 831 | 0.81 | 0.84 | 95 | ATP, 6R9, MG |
| 3 | 901 | 0.81 | 0.83 | 88 | ATP, 6R9, MG |
| 4 | 386 | 0.80 | 0.89 | 53 | ATP, 6R9, MG, EDO |
| 5 | 379 | 0.67 | 0.80 | 46 | empty |
Interfaces
3 interfaces between chains.
- B–C · 891 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 890 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 846 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5K8F · Crystal structure of Acetyl-CoA Synthetase in complex with ATP and Acetyl-AMP from… · 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 5K8F · PDBe 5K8F · UniProt J9VFT1
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