MolNFT v1 · #69344 · protein
Bacillus cereus metallo-beta-lactamase CYS221ASP mutant, 20 mm ZN(II)
3KNS · Beta-lactamase 2: “Bacillus cereus metallo-beta-lactamase CYS221ASP mutant, 20 mm ZN(II)”. X-ray diffraction, 2 ligands (ZN, SO4), 8 pockets (best druggability 0.70). MolNFT v1 #69344 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KNS
- Type
- protein
- Length
- 837 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase 2
- EC
- 3.5.2.6
- UniProt
- P04190
- Ligands
- ZN, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase 2 (EC 3.5.2.6) | protein | 214 | 27% helix, 34% strand | P04190 |
| B, D | Beta-lactamase 2 (EC 3.5.2.6) | protein | 205 | 28% helix, 31% strand | P04190 |
| C | Beta-lactamase 2 (EC 3.5.2.6) | protein | 213 | 27% helix, 34% strand | P04190 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D
- ACY · Acetic acid · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.70 | 0.81 | 66 | ACY |
| 2 | 327 | 0.66 | 0.81 | 49 | ZN, ACY |
| 3 | 211 | 0.58 | 0.80 | 35 | empty |
| 4 | 258 | 0.51 | 0.75 | 35 | empty |
| 5 | 162 | 0.46 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 598 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 594 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 556 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KNS · Bacillus cereus metallo-beta-lactamase Cys221Asp mutant, 20 mM Zn(II) · the same entry in another collection · chain D against D, 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 3KNS · PDBe 3KNS · UniProt P04190
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