Research workbench
Structure of pvdn from pseudomonas aeruginosa
Analyse Structure of pvdn from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HH9
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pvdn
- UniProt
- G3XCY5
- Ligands
- PLP
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pvdn | protein | 390 | 45% helix, 16% strand | G3XCY5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.83 | 0.97 | 58 | empty |
| 2 | 342 | 0.71 | 0.84 | 47 | PLP |
| 3 | 262 | 0.70 | 0.85 | 45 | PLP |
| 4 | 110 | 0.44 | 0.78 | 23 | empty |
| 5 | 68 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2726 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5HH9 · Structure of PvdN from Pseudomonas aeruginosa · 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 G3XCY5
- Elsewhere: RCSB PDB 5HH9 · PDBe 5HH9 · UniProt G3XCY5
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