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Crystal structure of phosphoglyceromutase from burkholderia pseudomallei with 3-phosphoglyceric acid and vanadate
Analyse Crystal structure of phosphoglyceromutase from burkholderia pseudomallei with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GP5
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
- EC
- 5.4.2.1
- UniProt
- Q63XU7
- Ligands
- 3PG, VO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 248 | 45% helix, 14% strand | Q63XU7 |
| B | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 229 | 43% helix, 15% strand | Q63XU7 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains A, B
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.61 | 0.81 | 43 | VO4, 3PG |
| 2 | 80 | 0.51 | 0.85 | 21 | VO4, 3PG |
| 3 | 152 | 0.40 | 0.73 | 19 | PG4 |
| 4 | 76 | 0.38 | 0.77 | 11 | empty |
| 5 | 50 | 0.34 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 881 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3GP5 · Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q63XU7 · AlphaFold monomer V2.0 prediction for 2,3-bisphosphoglycerate- dependent phosphoglycerate… · a predicted model of the same protein · chain B 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 Q63XU7
- Elsewhere: RCSB PDB 3GP5 · PDBe 3GP5 · UniProt Q63XU7
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