Research workbench
Structure of the periplasmic binding protein P5PA
Analyse Structure of the periplasmic binding protein P5PA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WCE
- Type
- protein
- Length
- 314 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.754
- Source
- Actinobacillus pleuropneumoniae
- Molecule
- Pyridoxal-5-phosphate binding protein A (P5PA)
- Ligands
- PLP
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.754 · 1 distinct chain · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal-5-phosphate binding protein A (P5PA) | protein | 314 | 48% helix, 21% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
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 | 288 | 0.72 | 0.86 | 36 | PLP |
| 2 | 105 | 0.48 | 0.80 | 20 | empty |
| 3 | 63 | 0.33 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WCE · Structure of the periplasmic binding protein P5PA · 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
- Elsewhere: RCSB PDB 6WCE · PDBe 6WCE
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