MolNFT v1 · #70820 · protein
New refinement of the crystal structure of bjp-1, a subclass B3 metallo-beta-lactamase of bradyrhizobium japonicum
3LVZ · BLR6230 protein: “New refinement of the crystal structure of bjp-1, a subclass B3 metallo-beta-lactamase of bradyrhizobium…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.53). MolNFT v1 #70820 on GenesisL1: 3D…
- PDB
- 3LVZ
- Type
- protein
- Length
- 545 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLR6230 protein
- UniProt
- Q89GW5
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BLR6230 protein | protein | 272 | 36% helix, 22% strand | Q89GW5 |
| B | BLR6230 protein | protein | 273 | 36% helix, 22% strand | Q89GW5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 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 | 314 | 0.53 | 0.74 | 40 | empty |
| 2 | 143 | 0.47 | 0.77 | 23 | ZN |
| 3 | 158 | 0.45 | 0.76 | 28 | ZN |
| 4 | 98 | 0.37 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 413 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3LVZ · New refinement of the crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of… · 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 3LVZ · PDBe 3LVZ · UniProt Q89GW5
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