Research workbench
Fragments bound to the oxa-48 beta-lactamase: compound 2
Analyse Fragments bound to the oxa-48 beta-lactamase: compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DTS
- Type
- protein
- Length
- 964 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
- 5F8, CL
- Pockets
- 14 · best druggability 0.75
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 | 241 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- 5F8 · 3-(pyridin-3-yl)benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.75 | 0.78 | 95 | empty |
| 2 | 343 | 0.63 | 0.79 | 44 | empty |
| 3 | 404 | 0.63 | 0.78 | 61 | empty |
| 4 | 158 | 0.43 | 0.74 | 27 | 5F8 |
| 5 | 131 | 0.40 | 0.74 | 22 | 5F8 |
Interfaces
5 interfaces between chains.
- B–C · 352 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 212 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 108 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5DTS · Fragments bound to the OXA-48 beta-lactamase: Compound 2 · 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 5DTS · PDBe 5DTS · UniProt Q6XEC0
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