MolNFT v1 · #83747 · protein
N288Q-N321Q mutant beta-lactamase derived from chromohalobacter SP.560 (without soaking)
3WRZ: “N288Q-N321Q mutant beta-lactamase derived from chromohalobacter SP.560 (without soaking)”. X-ray diffraction, 2 ligands (CA, CL), 9 pockets (best druggability 0.74). MolNFT v1 #83747 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3WRZ
- Type
- protein
- Length
- 1,070 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
- CA, CL
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 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, 20% strand | Q76LX5 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 40% helix, 20% strand | Q76LX5 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 40% helix, 19% strand | Q76LX5 |
Ligands and binding sites
- CA · Calcium ion · metal · 11 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
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 | 980 | 0.74 | 0.78 | 94 | CA, CL |
| 2 | 790 | 0.71 | 0.77 | 71 | empty |
| 3 | 285 | 0.59 | 0.78 | 45 | CL |
| 4 | 308 | 0.59 | 0.77 | 41 | CL |
| 5 | 50 | 0.32 | 0.77 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 402 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 399 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3WRZ · N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (without soaking) · 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 3WRZ · PDBe 3WRZ · UniProt Q76LX5
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