MolNFT v1 · #64999 · protein
Crystal structure of pyridoxal phosphate biosynthetic protein from burkholderia pseudomallei
3GK0 · Pyridoxine 5'-phosphate synthase: “Crystal structure of pyridoxal phosphate biosynthetic protein from burkholderia pseudomallei”. X-ray diffraction, 2 ligands (DXP, PO4), 11 pockets (best druggability 0.77). MolNFT v1 #64999 on…
- PDB
- 3GK0
- Type
- protein
- Length
- 1,974 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine 5'-phosphate synthase
- EC
- 2.6.99.2
- UniProt
- Q3JQ80
- Ligands
- DXP, PO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 252 | 51% helix, 16% strand | Q3JQ80 |
| C, F | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 244 | 49% helix, 17% strand | Q3JQ80 |
| D, H | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 246 | 50% helix, 17% strand | Q3JQ80 |
| E, G | Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) | protein | 245 | 51% helix, 17% strand | Q3JQ80 |
Ligands and binding sites
- DXP · 1-deoxy-D-xylulose-5-phosphate · ligand · 3 copies · chains C, H, D, F, A, G
- PO4 · Phosphate ion · ion · 5 copies · chains B, E, D, F, A, G, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.77 | 0.80 | 71 | PO4 |
| 2 | 671 | 0.74 | 0.80 | 80 | PO4 |
| 3 | 933 | 0.74 | 0.78 | 76 | PO4 |
| 4 | 510 | 0.72 | 0.81 | 55 | PO4 |
| 5 | 404 | 0.69 | 0.81 | 44 | PO4 |
Interfaces
10 interfaces between chains.
- B–E · 1066 Ų buried · 8 hydrogen bonds · protein-protein
- C–H · 1066 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 1064 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 1061 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 802 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3GK0 · Crystal structure of pyridoxal phosphate biosynthetic protein from Burkholderia… · the same entry in another collection · chain H against H, TM-score 1.00
- Q3JQ80 · AlphaFold monomer V2.0 prediction for pyridoxine 5'-phosphate synthase (Q3JQ80) · a predicted model of the same protein · chain C 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 Q3JQ80
- Elsewhere: RCSB PDB 3GK0 · PDBe 3GK0 · UniProt Q3JQ80
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.