MolNFT v1 · #158032 · protein
Crystal structure of the beta lactamase class a penp from bacillus subtilis
6NI1 · Beta-lactamase: “Crystal structure of the beta lactamase class a penp from bacillus subtilis”. X-ray diffraction, 5 pockets (best druggability 0.61). MolNFT v1 #158032 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NI1
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A1Y0WMN3
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 269 | 45% helix, 18% strand | A0A1Y0WMN3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.61 | 0.77 | 45 | FMT |
| 2 | 55 | 0.41 | 0.82 | 22 | FMT |
| 3 | 53 | 0.36 | 0.80 | 15 | EDO, FMT |
| 4 | 70 | 0.27 | 0.73 | 18 | empty |
| 5 | 58 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 367 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NI1 · Crystal Structure of the Beta Lactamase Class A penP from Bacillus subtilis · 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 A0A1Y0WMN3
- Elsewhere: RCSB PDB 6NI1 · PDBe 6NI1 · UniProt A0A1Y0WMN3
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