Research workbench
Oxa-48 in complex with compound 19A
Analyse Oxa-48 in complex with compound 19A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QAN
- Type
- protein
- Length
- 971 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
- M8Q, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 22% strand | Q6XEC0 |
| B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 22% strand | Q6XEC0 |
Ligands and binding sites
- M8Q · 3-[3-(methylsulfonylaminomethyl)phenyl]benzoic acid · ligand · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.80 | 0.88 | 78 | CL |
| 2 | 967 | 0.79 | 0.81 | 94 | empty |
| 3 | 529 | 0.73 | 0.81 | 73 | M8Q |
| 4 | 177 | 0.44 | 0.74 | 35 | M8Q |
| 5 | 63 | 0.34 | 0.77 | 20 | M8Q |
Interfaces
4 interfaces between chains.
- A–D · 999 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 223 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAN · OXA-48 IN COMPLEX WITH COMPOUND 19a · 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 5QAN · PDBe 5QAN · UniProt Q6XEC0
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