MolNFT v1 · #46270 · protein
Structure of beta-lactamase II from bacillus cereus. R121H, C221S double mutant. space group P3121.
2NZE: “Structure of beta-lactamase II from bacillus cereus. R121H, C221S double mutant. space group P3121.”. X-ray diffraction, 2 ligands (ZN, SO4), 2 pockets (best druggability 0.40). MolNFT v1 #46270 on GenesisL1: 3D structure, binding…
- PDB
- 2NZE
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase II
- EC
- 3.5.2.6
- UniProt
- P04190
- Ligands
- ZN, SO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase II (EC 3.5.2.6) | protein | 215 | 27% helix, 32% strand | P04190 |
| B | Beta-lactamase II (EC 3.5.2.6) | protein | 217 | 27% helix, 32% strand | P04190 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- ACY · Acetic acid · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.40 | 0.77 | 23 | SO4 |
| 2 | 91 | 0.35 | 0.75 | 21 | SO4 |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2NZE · Structure of beta-lactamase II from Bacillus cereus. R121H, C221S double mutant. Space… · 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 B against A, TM-score 0.99
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 2NZE · PDBe 2NZE · UniProt P04190
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