MolNFT v1 · #60731 · protein
Crystal structure of the lpqc, POLY(3-hydroxybutyrate) depolymerase from bordetella parapertussis
3D0K · Putative POLY(3-hydroxybutyrate) depolymerase lpqc: “Crystal structure of the lpqc, POLY(3-hydroxybutyrate) depolymerase from bordetella parapertussis”. X-ray diffraction, 2 ligands (SO4, CL), 5 pockets (best druggability 0.40).…
- PDB
- 3D0K
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative POLY(3-hydroxybutyrate) depolymerase lpqc
- UniProt
- Q7W3B7
- Ligands
- SO4, CL
- Pockets
- 5 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative POLY(3-hydroxybutyrate) depolymerase lpqc | protein | 287 | 37% helix, 17% strand | Q7W3B7 |
| B | Putative POLY(3-hydroxybutyrate) depolymerase lpqc | protein | 293 | 38% helix, 17% strand | Q7W3B7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.40 | 0.75 | 28 | SO4 |
| 2 | 65 | 0.37 | 0.79 | 12 | empty |
| 3 | 64 | 0.36 | 0.78 | 11 | empty |
| 4 | 73 | 0.35 | 0.76 | 19 | SO4 |
| 5 | 70 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 424 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3D0K · Crystal structure of the LpqC, poly(3-hydroxybutyrate) depolymerase from Bordetella… · 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 Q7W3B7
- Elsewhere: RCSB PDB 3D0K · PDBe 3D0K · UniProt Q7W3B7
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