MolNFT v1 · #131654 · protein
Oxa-48 in complex with compound 34
5QAZ · Beta-lactamase: “Oxa-48 in complex with compound 34”. X-ray diffraction, 2 ligands (Q2S, CL), 10 pockets (best druggability 0.79). MolNFT v1 #131654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QAZ
- Type
- protein
- Length
- 968 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
- Q2S, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- Q2S · 3-(1~{H}-indol-5-yl)benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.79 | 0.82 | 87 | empty |
| 2 | 602 | 0.74 | 0.81 | 79 | empty |
| 3 | 183 | 0.50 | 0.77 | 27 | empty |
| 4 | 109 | 0.36 | 0.74 | 23 | Q2S |
| 5 | 50 | 0.36 | 0.80 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 490 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 385 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 299 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAZ · Oxa-48 in complex with compound 34 · 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 Q6XEC0
- Elsewhere: RCSB PDB 5QAZ · PDBe 5QAZ · UniProt Q6XEC0
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