MolNFT v1 · #168128 · protein
Crystal structure of a pyridoxine 5'-phosphate synthease from stenotrophomonas maltophilia K279A
6W6A · Pyridoxine 5'-phosphate synthase: “Crystal structure of a pyridoxine 5'-phosphate synthease from stenotrophomonas maltophilia K279A”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.64). MolNFT v1 #168128 on…
- PDB
- 6W6A
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine 5'-phosphate synthase
- EC
- 2.6.99.2
- UniProt
- B2FT93
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 249 | 45% helix, 17% strand | B2FT93 |
| B | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 246 | 46% helix, 17% strand | B2FT93 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.64 | 0.88 | 32 | PO4 |
| 2 | 112 | 0.51 | 0.82 | 21 | empty |
| 3 | 156 | 0.45 | 0.76 | 23 | empty |
| 4 | 134 | 0.41 | 0.75 | 20 | empty |
| 5 | 52 | 0.25 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1138 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6W6A · Crystal structure of a pyridoxine 5'-phosphate synthease from Stenotrophomonas… · 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 B2FT93
- Elsewhere: RCSB PDB 6W6A · PDBe 6W6A · UniProt B2FT93
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