MolNFT v1 · #117248 · protein
Crystal structure of beta-lactamase class D from bacillus subtilis
5E2F · Beta-lactamase ybxi: “Crystal structure of beta-lactamase class D from bacillus subtilis”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.75). MolNFT v1 #117248 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5E2F
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ybxi
- EC
- 3.5.2.6
- UniProt
- P54427
- Ligands
- CA
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase ybxi (EC 3.5.2.6) | protein | 237 | 38% helix, 21% strand | P54427 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.75 | 0.82 | 50 | empty |
| 2 | 222 | 0.50 | 0.75 | 46 | empty |
| 3 | 190 | 0.47 | 0.75 | 34 | EDO |
Interfaces
1 interface between chains.
- A–B · 1085 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered, acetylation).
Compared structures
- 5E2F · Crystal Structure of Beta-lactamase class D from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P54427 · AlphaFold monomer V2.0 prediction for probable beta-lactamase ybxi (P54427) · 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 P54427
- Elsewhere: RCSB PDB 5E2F · PDBe 5E2F · UniProt P54427
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