MolNFT v1 · #11753 · protein
Structure of cephalosporin acylase in complex with glutaryl- 7-aminocephalosporanic acid
1JVZ · Cephalosporin acylase alpha chain: “Structure of cephalosporin acylase in complex with glutaryl- 7-aminocephalosporanic acid”. X-ray diffraction, 1 ligand (CEN), 5 pockets (best druggability 0.63). MolNFT v1 #11753 on GenesisL1: 3D…
- PDB
- 1JVZ
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cephalosporin acylase alpha chain; Cephalosporin acylase beta chain
- UniProt
- Q9L5D6
- Ligands
- CEN
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cephalosporin acylase alpha chain | protein | 152 | 69% helix, 6% strand | Q9L5D6 |
| B | Cephalosporin acylase beta chain | protein | 520 | 26% helix, 29% strand | Q9L5D6 |
Ligands and binding sites
- CEN · 7beta-(4carboxybutanamido) cephalosporanic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.63 | 0.78 | 75 | CEN |
| 2 | 161 | 0.51 | 0.79 | 26 | empty |
| 3 | 57 | 0.36 | 0.79 | 19 | empty |
| 4 | 106 | 0.34 | 0.73 | 28 | empty |
| 5 | 79 | 0.32 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 4059 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 1JVZ · Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid · the same entry in another collection · chain B against B, TM-score 1.00
- Q9L5D6 · AlphaFold monomer V2.0 prediction for glutaryl-7-aminocephalosporanic-acid acylase… · a predicted model of the same protein · chain B 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 Q9L5D6
- Elsewhere: RCSB PDB 1JVZ · PDBe 1JVZ · UniProt Q9L5D6
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