MolNFT v1 · #112394 · protein
Crystal structure of a benzoate coenzyme a ligase with benzoyl-AMP
4ZJZ · Benzoate-coenzyme a ligase: “Crystal structure of a benzoate coenzyme a ligase with benzoyl-AMP”. X-ray diffraction, 2 ligands (OOB, BEZ), 6 pockets (best druggability 0.81). MolNFT v1 #112394 on GenesisL1: 3D structure, binding…
- PDB
- 4ZJZ
- Type
- protein
- Length
- 1,036 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoate-coenzyme a ligase
- UniProt
- Q93TK0
- Ligands
- OOB, BEZ
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoate-coenzyme a ligase | protein | 517 | 31% helix, 25% strand | Q93TK0 |
| B | Benzoate-coenzyme a ligase | protein | 519 | 30% helix, 26% strand | Q93TK0 |
Ligands and binding sites
- OOB · 5'-O-[(R)-(benzoyloxy)(hydroxy)phosphoryl]adenosine · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.81 | 0.83 | 109 | BEZ, OOB, GOL |
| 2 | 982 | 0.81 | 0.82 | 115 | OOB, BEZ, GOL |
| 3 | 822 | 0.74 | 0.78 | 77 | GOL |
| 4 | 153 | 0.51 | 0.79 | 19 | empty |
| 5 | 119 | 0.50 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 490 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4ZJZ · Crystal structure of a benzoate coenzyme A ligase with Benzoyl-AMP · 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 Q93TK0
- Elsewhere: RCSB PDB 4ZJZ · PDBe 4ZJZ · UniProt Q93TK0
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