MolNFT v1 · #123524 · protein
Crystal structure of bcii metallo-beta-lactamase in complex with dz- 305
5JMX · Metallo-beta-lactamase type 2: “Crystal structure of bcii metallo-beta-lactamase in complex with dz- 305”. X-ray diffraction, 3 ligands (DZ5, ZN, SO4), 1 pocket (best druggability 0.28). MolNFT v1 #123524 on GenesisL1: 3D structure…
- PDB
- 5JMX
- Type
- protein
- Length
- 217 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- P04190
- Ligands
- DZ5, ZN, SO4
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 217 | 27% helix, 31% strand | P04190 |
Ligands and binding sites
- DZ5 · (2Z)-3-(4-fluorophenyl)-2-sulfanylprop-2-enoic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.28 | 0.75 | 15 | ZN, DZ5 |
Compared structures
- 5JMX · Crystal Structure of BcII metallo-beta-lactamase in complex with DZ-305 · the same entry in another collection · chain A against A, TM-score 1.00
- P04190 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (P04190) · a predicted model of the same protein · 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 P04190
- Elsewhere: RCSB PDB 5JMX · PDBe 5JMX · UniProt P04190
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