Research workbench
X-ray crystal structure of a pyridoxine 5-prime-phosphate synthase from pseudomonas aeruginosa
Analyse X-ray crystal structure of a pyridoxine 5-prime-phosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DLC
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine 5'-phosphate synthase
- EC
- 2.6.99.2
- UniProt
- Q02HS5
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 242 | 50% helix, 16% strand | Q02HS5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.65 | 0.80 | 38 | PO4 |
| 2 | 246 | 0.62 | 0.81 | 28 | empty |
| 3 | 223 | 0.62 | 0.82 | 28 | empty |
| 4 | 228 | 0.61 | 0.81 | 26 | empty |
| 5 | 82 | 0.35 | 0.75 | 12 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1266 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1146 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5DLC · X-ray Crystal Structure of a Pyridoxine 5-prime-phosphate synthase from Pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02HS5 · AlphaFold monomer V2.0 prediction for pyridoxine 5'-phosphate synthase (Q02HS5) · 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 Q02HS5
- Elsewhere: RCSB PDB 5DLC · PDBe 5DLC · UniProt Q02HS5
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