Research workbench
N288Q-N321Q mutant beta-lactamase derived from chromohalobacter SP.560 (condition-2A)
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
- 3WS4
- Type
- protein
- Length
- 1,074 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q76LX5
- Ligands
- SR, CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 39% helix, 20% strand | Q76LX5 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 39% helix, 20% strand | Q76LX5 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 39% helix, 20% strand | Q76LX5 |
Ligands and binding sites
- SR · Strontium ion · metal · 8 copies · chains A, B, C
- 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 | 1027 | 0.74 | 0.77 | 103 | SR, CL |
| 2 | 882 | 0.70 | 0.76 | 70 | SR |
| 3 | 269 | 0.57 | 0.78 | 41 | CL |
| 4 | 266 | 0.55 | 0.77 | 39 | CL |
| 5 | 50 | 0.31 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 377 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3WS4 · N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-2A) · 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 3WS4 · PDBe 3WS4 · UniProt Q76LX5
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