Research workbench
Oxa-48 in complex with compound 4C
Analyse Oxa-48 in complex with compound 4C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QA8
- 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
- JSX, CL
- Pockets
- 6 · best druggability 0.77
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
- JSX · 3-(4-hydroxyphenyl)benzoic acid · ligand · 3 copies · chains A, C, D
- CL · Chloride ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.77 | 0.80 | 129 | JSX |
| 2 | 881 | 0.77 | 0.80 | 127 | CL, JSX |
| 3 | 142 | 0.48 | 0.78 | 24 | empty |
| 4 | 193 | 0.44 | 0.74 | 28 | empty |
| 5 | 50 | 0.37 | 0.81 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 969 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 968 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 374 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 177 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QA8 · OXA-48 IN COMPLEX WITH COMPOUND 4c · 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 5QA8 · PDBe 5QA8 · UniProt Q6XEC0
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