MolNFT v2 · #86412 · protein
Crystal structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa
4B52 · Bacillolysin: “Crystal structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa”. X-ray diffraction at 1.76, 4 ligands (RDF, CA, ZN), 3 pockets (best druggability 0.77). MolNFT v2 #86412 on GenesisL1: 3D…
- PDB
- 4B52
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.76
- Source
- PAENIBACILLUS POLYMYXA
- Molecule
- Bacillolysin
- EC
- 3.4.24.4
- UniProt
- E3E6L0
- Ligands
- RDF, CA, ZN, NA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.76 · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacillolysin (EC 3.4.24.4) | protein | 304 | 43% helix, 18% strand | E3E6L0 |
Ligands and binding sites
- RDF · N-alpha-L-rhamnopyranosyloxy(hydroxyphosphinyl)-L-leucyl-L-tryptophan · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 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 | 896 | 0.77 | 0.80 | 84 | RDF, NA |
| 2 | 116 | 0.44 | 0.78 | 30 | empty |
| 3 | 91 | 0.43 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4B52 · Crystal structure of gentlyase, the neutral metalloprotease of paenibacillus polymyxa · 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 E3E6L0
- Elsewhere: RCSB PDB 4B52 · PDBe 4B52 · UniProt E3E6L0
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