MolNFT v1 · #168019 · protein
Crystal structure of the beta lactamase class a penp from bacillus subtilis in the complex with the non-beta- lactam beta-lactamase inhibitor avibactam
6W2Z: “Crystal structure of the beta lactamase class a penp from bacillus subtilis in the complex with the non-beta…”. X-ray diffraction, 1 ligand (NXL), 5 pockets (best druggability 0.51). MolNFT v1 #168019 on GenesisL1: 3D structure…
- PDB
- 6W2Z
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P39824
- Ligands
- NXL
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 260 | 46% helix, 18% strand | P39824 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 261 | 45% helix, 19% strand | P39824 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
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 | 266 | 0.51 | 0.75 | 41 | empty |
| 2 | 190 | 0.43 | 0.73 | 31 | NXL |
| 3 | 58 | 0.38 | 0.80 | 20 | empty |
| 4 | 59 | 0.37 | 0.79 | 16 | empty |
| 5 | 75 | 0.30 | 0.74 | 18 | NXL |
Interfaces
1 interface between chains.
- A–B · 204 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6W2Z · Crystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the… · the same entry in another collection · chain A against A, TM-score 1.00
- P39824 · AlphaFold monomer V2.0 prediction for beta-lactamase (P39824) · a predicted model of the same protein · chain B 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 P39824
- Elsewhere: RCSB PDB 6W2Z · PDBe 6W2Z · UniProt P39824
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