Research workbench
Crystal structure of acetyl-CoA synthetase in complex with adenosine- 5'-butylphosphate from cryptococcus neoformans var. grubii serotype a (H99)
Analyse Crystal structure of acetyl-CoA synthetase in complex with adenosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KNP
- Type
- protein
- Length
- 1,822 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
- WT7, PO4
- Pockets
- 18 · 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 | 653 | 33% helix, 23% strand | J9VFT1 |
| B | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 658 | 32% helix, 22% strand | J9VFT1 |
| C | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 511 | 32% helix, 23% strand | J9VFT1 |
Ligands and binding sites
- WT7 · 5'-O-[(S)-butoxy(hydroxy)phosphoryl]adenosine · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.88 | 0.90 | 133 | EDO |
| 2 | 975 | 0.82 | 0.83 | 107 | WT7 |
| 3 | 1062 | 0.80 | 0.81 | 90 | WT7 |
| 4 | 427 | 0.70 | 0.81 | 66 | WT7 |
| 5 | 289 | 0.61 | 0.79 | 42 | empty |
Interfaces
3 interfaces between chains.
- B–C · 868 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 868 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 857 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7KNP · Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-butylphosphate… · 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 7KNP · PDBe 7KNP · UniProt J9VFT1
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