MolNFT v1 · #29362 · protein
Crystal structure of penicillin-binding protein 5 from E. COLI in complex with a boronic acid inhibitor
1Z6F: “Crystal structure of penicillin-binding protein 5 from E. COLI in complex with a boronic acid inhibitor”. X-ray diffraction, 1 ligand (BO9), 3 pockets (best druggability 0.45). MolNFT v1 #29362 on GenesisL1: 3D structure, binding…
- PDB
- 1Z6F
- Type
- protein
- Length
- 354 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 5
- EC
- 3.4.16.4
- UniProt
- P04287
- Ligands
- BO9
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 5 (EC 3.4.16.4) | protein | 354 | 29% helix, 32% strand | P04287 |
Ligands and binding sites
- BO9 · N1-[(1R)-1-(dihydroxyboryl)ethyl]-N2-[(tert-butoxycarbonyl)-D-gamma-glutamyl]-N6-[(benzyloxy)carbonyl-L-lysinamide · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.45 | 0.74 | 25 | empty |
| 2 | 121 | 0.43 | 0.77 | 27 | empty |
| 3 | 62 | 0.27 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1Z6F · Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic… · 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 P04287
- Elsewhere: RCSB PDB 1Z6F · PDBe 1Z6F · UniProt P04287
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