MolNFT v1 · #131658 · protein
Oxa-48 in complex with compound 40
5QB3 · Beta-lactamase: “Oxa-48 in complex with compound 40”. X-ray diffraction, 2 ligands (AVM, CL), 9 pockets (best druggability 0.73). MolNFT v1 #131658 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QB3
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- AVM, CL
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- AVM · 3-(3-acetamidophenyl)-5-quinolin-7-yl-benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.73 | 0.81 | 81 | AVM |
| 2 | 474 | 0.73 | 0.82 | 57 | empty |
| 3 | 211 | 0.61 | 0.82 | 35 | empty |
| 4 | 202 | 0.51 | 0.76 | 28 | empty |
| 5 | 123 | 0.38 | 0.74 | 22 | AVM |
Interfaces
4 interfaces between chains.
- A–B · 476 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 261 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 251 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QB3 · Oxa-48 in complex with compound 40 · 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 Q6XEC0
- Elsewhere: RCSB PDB 5QB3 · PDBe 5QB3 · UniProt Q6XEC0
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