MolNFT v1 · #180582 · protein
Crystal structure of acetyl-CoA synthetase in complex with acetyl adenylate from cryptococcus neoformans H99
7L4G · Acetyl-coenzyme a synthetase: “Crystal structure of acetyl-CoA synthetase in complex with acetyl adenylate from cryptococcus neoformans H99”. X-ray diffraction, 3 ligands (6R9, K, PO4), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 7L4G
- Type
- protein
- Length
- 1,954 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
- 6R9, K, PO4
- Pockets
- 20 · best druggability 0.89
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 | 656 | 32% helix, 23% strand | J9VFT1 |
| B | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 668 | 32% helix, 22% strand | J9VFT1 |
| C | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 630 | 33% helix, 24% strand | J9VFT1 |
Ligands and binding sites
- 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
- K · Potassium ion · metal · chains C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C
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 | 1101 | 0.89 | 0.90 | 137 | EDO |
| 2 | 609 | 0.80 | 0.86 | 70 | 6R9 |
| 3 | 678 | 0.79 | 0.83 | 81 | 6R9, K |
| 4 | 496 | 0.77 | 0.85 | 54 | 6R9 |
| 5 | 441 | 0.71 | 0.81 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–B · 881 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 875 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7L4G · Crystal Structure of Acetyl-CoA synthetase in complex with acetyl adenylate 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 7L4G · PDBe 7L4G · UniProt J9VFT1
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