MolNFT v1 · #179705 · protein
Crystal structure of acetyl-CoA synthetase in complex with adenosine- 5'-propylphosphate from aspergillus fumigatus
7KDN · Acetyl-coenzyme a synthetase: “Crystal structure of acetyl-CoA synthetase in complex with adenosine- 5'-propylphosphate from aspergillus…”. X-ray diffraction, 1 ligand (PRX), 20 pockets (best druggability 0.82). MolNFT v1 #179705 on…
- PDB
- 7KDN
- Type
- protein
- Length
- 3,499 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-coenzyme a synthetase
- EC
- 6.2.1.1
- UniProt
- Q4WQ02
- Ligands
- PRX
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 622 | 32% helix, 24% strand | Q4WQ02 |
| B | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 575 | 33% helix, 24% strand | Q4WQ02 |
| C | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 518 | 33% helix, 22% strand | Q4WQ02 |
| D | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 590 | 33% helix, 23% strand | Q4WQ02 |
| E | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 605 | 32% helix, 24% strand | Q4WQ02 |
| F | Acetyl-coenzyme a synthetase (EC 6.2.1.1) | protein | 589 | 32% helix, 24% strand | Q4WQ02 |
Ligands and binding sites
- PRX · Adenosine-5'-monophosphate-propyl ester · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.82 | 0.84 | 90 | PRX |
| 2 | 1068 | 0.82 | 0.83 | 111 | PRX |
| 3 | 841 | 0.81 | 0.84 | 97 | PRX |
| 4 | 846 | 0.81 | 0.84 | 107 | PRX |
| 5 | 1053 | 0.80 | 0.81 | 99 | PRX |
Interfaces
9 interfaces between chains.
- B–D · 782 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 753 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 312 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 262 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7KDN · 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 Q4WQ02
- Elsewhere: RCSB PDB 7KDN · PDBe 7KDN · UniProt Q4WQ02
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