MolNFT v1 · #128217 · protein
Crystal structure of bjp-1 metallo beta-lactamase in complex with boric acid
5NJW · BLR6230 protein: “Crystal structure of bjp-1 metallo beta-lactamase in complex with boric acid”. X-ray diffraction, 3 ligands (ZN, BO3, OH), 5 pockets (best druggability 0.53). MolNFT v1 #128217 on GenesisL1: 3D structure, binding…
- PDB
- 5NJW
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLR6230 protein
- UniProt
- Q89GW5
- Ligands
- ZN, BO3, OH
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | BLR6230 protein | protein | 274 | 35% helix, 22% strand | Q89GW5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
- BO3 · Boric acid · ion · 2 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.53 | 0.75 | 42 | BO3, OH |
| 2 | 285 | 0.51 | 0.74 | 33 | empty |
| 3 | 173 | 0.50 | 0.77 | 31 | ZN, BO3, OH |
| 4 | 100 | 0.37 | 0.75 | 17 | empty |
| 5 | 53 | 0.28 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 422 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5NJW · Crystal Structure of BJP-1 metallo beta-lactamase in complex with boric acid · 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 Q89GW5
- Elsewhere: RCSB PDB 5NJW · PDBe 5NJW · UniProt Q89GW5
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