Research workbench
Bacillus cereus metallo-beta-lactamase (bcii) arg (121) cys mutant. solved at PH5 using 20 micromolar ZNSO4 in the buffer. 1MM dtt was used as a reducing agent. CYS221 is oxidized.
Analyse Bacillus cereus metallo-beta-lactamase (bcii) arg (121) cys mutant. solved at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BG6
- Type
- protein
- Length
- 434 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, AZI
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase II (EC 3.5.2.6) | protein | 216 | 26% helix, 32% strand | P04190 |
| B | Beta-lactamase II (EC 3.5.2.6) | protein | 218 | 27% helix, 33% strand | P04190 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 16 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 | 108 | 0.36 | 0.74 | 22 | AZI |
| 2 | 56 | 0.27 | 0.73 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2BG6 · Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH5 using… · 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 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 2BG6 · PDBe 2BG6 · UniProt P04190
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