Research workbench
Fragments bound to the oxa-48 beta-lactamase: compound 3
Analyse Fragments bound to the oxa-48 beta-lactamase: compound 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DTT
- 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
- 5F5, CL
- Pockets
- 9 · 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 | 242 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- 5F5 · 3-(1,3-thiazol-2-yl)benzoic acid · ligand · 2 copies · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.75 | 0.81 | 91 | empty |
| 2 | 504 | 0.73 | 0.82 | 61 | empty |
| 3 | 295 | 0.69 | 0.83 | 43 | empty |
| 4 | 190 | 0.51 | 0.77 | 26 | empty |
| 5 | 106 | 0.36 | 0.74 | 24 | 5F5 |
Interfaces
5 interfaces between chains.
- A–B · 486 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 419 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 326 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 271 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5DTT · Fragments bound to the OXA-48 beta-lactamase: Compound 3 · 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 5DTT · PDBe 5DTT · UniProt Q6XEC0
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