Research workbench
Oxa-48 in complex with compound 6B
Analyse Oxa-48 in complex with compound 6B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QAB
- Type
- protein
- Length
- 966 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
- XEV, CL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 20% strand | Q6XEC0 |
| B, C | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 40% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- XEV · 3-(3-methoxyphenyl)benzoic acid · ligand · 3 copies · chains A, B, D
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.72 | 0.81 | 68 | XEV |
| 2 | 450 | 0.72 | 0.82 | 53 | empty |
| 3 | 358 | 0.64 | 0.79 | 39 | EDO |
| 4 | 167 | 0.47 | 0.76 | 26 | empty |
| 5 | 103 | 0.36 | 0.74 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 515 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 375 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 341 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 268 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAB · OXA-48 IN COMPLEX WITH COMPOUND 6b · 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 5QAB · PDBe 5QAB · UniProt Q6XEC0
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