Research workbench
Oxa-48 in complex with compound 35
Analyse Oxa-48 in complex with compound 35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QB0
- 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
- AVA, CL
- Pockets
- 7 · best druggability 0.76
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 | 242 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- AVA · 3-pyridin-2-ylbenzoic acid · ligand · 4 copies · chains A, B, D
- CL · Chloride ion · ion · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.76 | 0.81 | 93 | AVA, EDO |
| 2 | 501 | 0.73 | 0.82 | 64 | empty |
| 3 | 255 | 0.64 | 0.81 | 36 | empty |
| 4 | 195 | 0.53 | 0.78 | 27 | empty |
| 5 | 166 | 0.44 | 0.75 | 29 | AVA |
Interfaces
5 interfaces between chains.
- A–B · 488 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 351 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 289 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 267 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QB0 · Oxa-48 in complex with compound 35 · 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 5QB0 · PDBe 5QB0 · UniProt Q6XEC0
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