MolNFT v1 · #141517 · protein
Fox-4 beta-lactamase complexed with avibactam
5ZA2: “Fox-4 beta-lactamase complexed with avibactam”. X-ray diffraction, 1 ligand (NXL), 5 pockets (best druggability 0.77). MolNFT v1 #141517 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZA2
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9L387
- Ligands
- NXL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 354 | 39% helix, 23% strand | Q9L387 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 41% helix, 23% strand | Q9L387 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
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 | 1195 | 0.77 | 0.79 | 112 | NXL, EPE |
| 2 | 301 | 0.57 | 0.77 | 35 | GOL |
| 3 | 139 | 0.47 | 0.78 | 35 | NXL |
| 4 | 97 | 0.46 | 0.80 | 17 | empty |
| 5 | 59 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 5ZA2 · Fox-4 beta-lactamase complexed with avibactam · the same entry in another collection · chain B against B, 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 Q9L387
- Elsewhere: RCSB PDB 5ZA2 · PDBe 5ZA2 · UniProt Q9L387
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