MolNFT v1 · #122112 · protein
Crystal structure of acetyl-CoA synthetase in complex with adenosine- 5'-propylphosphate from cryptococcus neoformans H99
5IFI · Acetyl-coenzyme a synthetase: “Crystal structure of acetyl-CoA synthetase in complex with adenosine- 5'-propylphosphate from cryptococcus…”. X-ray diffraction, 2 ligands (PRX, PO4), 18 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 5IFI
- Type
- protein
- Length
- 1,859 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
- PRX, PO4
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 650 | 33% helix, 23% strand | J9VFT1 |
| B | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 642 | 33% helix, 24% strand | J9VFT1 |
| C | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 567 | 32% helix, 24% strand | J9VFT1 |
Ligands and binding sites
- PRX · Adenosine-5'-monophosphate-propyl ester · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains B
- EDO · 1,2-ethanediol · additive · 18 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.89 | 0.90 | 138 | EDO |
| 2 | 902 | 0.81 | 0.83 | 86 | PRX |
| 3 | 861 | 0.80 | 0.82 | 103 | PRX |
| 4 | 875 | 0.79 | 0.82 | 90 | PRX |
| 5 | 138 | 0.65 | 0.87 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 865 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 856 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 846 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5IFI · Crystal structure of acetyl-CoA synthetase in complex with adenosine-5'-propylphosphate… · 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 5IFI · PDBe 5IFI · UniProt J9VFT1
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