Research workbench
Crystal structure of phosphoglycerate kinase from campylobacter jejuni.
Analyse Crystal structure of phosphoglycerate kinase from campylobacter jejuni. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q3V
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- Q9PMQ5
- Ligands
- K, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 394 | 42% helix, 16% strand | Q9PMQ5 |
| B | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 392 | 41% helix, 17% strand | Q9PMQ5 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.77 | 0.83 | 70 | empty |
| 2 | 330 | 0.65 | 0.80 | 35 | empty |
| 3 | 105 | 0.55 | 0.84 | 25 | K |
| 4 | 149 | 0.46 | 0.77 | 37 | FMT |
| 5 | 177 | 0.46 | 0.75 | 35 | SO4 |
Interfaces
1 interface between chains.
- A–B · 668 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3Q3V · Crystal structure of Phosphoglycerate Kinase from Campylobacter jejuni. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PMQ5 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (Q9PMQ5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9PMQ5
- Elsewhere: RCSB PDB 3Q3V · PDBe 3Q3V · UniProt Q9PMQ5
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