Research workbench
Crystal structure of the complex between class B3 beta-lactamase bjp-1 and 4-nitrobenzene-sulfonamide - new refinement
Analyse Crystal structure of the complex between class B3 beta-lactamase bjp-1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WCM
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLR6230 protein
- UniProt
- Q89GW5
- Ligands
- 4NZ, ZN
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | BLR6230 protein | protein | 263 | 34% helix, 23% strand | Q89GW5 |
Ligands and binding sites
- 4NZ · 4-nitrobenzenesulfonamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.55 | 0.76 | 38 | empty |
| 2 | 82 | 0.36 | 0.76 | 18 | 4NZ |
| 3 | 67 | 0.35 | 0.77 | 15 | empty |
| 4 | 73 | 0.35 | 0.76 | 18 | ZN, 4NZ |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5WCM · Crystal structure of the complex between class B3 beta-lactamase BJP-1 and… · the same entry in another collection · chain B against B, 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 Q89GW5
- Elsewhere: RCSB PDB 5WCM · PDBe 5WCM · UniProt Q89GW5
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