Research workbench
N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-2B)
Analyse N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WS5
- Type
- protein
- Length
- 1,073 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Chromohalobacter sp. 560
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q76LX5
- Ligands
- SR, CA, CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 40% helix, 21% strand | Q76LX5 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 40% helix, 19% strand | Q76LX5 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 40% helix, 19% strand | Q76LX5 |
Ligands and binding sites
- SR · Strontium ion · metal · chains A
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.74 | 0.77 | 97 | CL |
| 2 | 754 | 0.69 | 0.76 | 72 | empty |
| 3 | 293 | 0.56 | 0.76 | 43 | CL |
| 4 | 290 | 0.56 | 0.76 | 40 | CL |
| 5 | 51 | 0.27 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 388 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 326 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3WS5 · N288Q-N321Q mutant beta-lactamase derived from chromohalobacter SP.560 (condition-2B) · 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 Q76LX5
- Elsewhere: RCSB PDB 3WS5 · PDBe 3WS5 · UniProt Q76LX5
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