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Crystal structure of phosphoglyceromutase from burkholderia pseudomallei with 2-phosphoserine
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
- 3GP3
- Type
- protein
- Length
- 918 residues
- Chains
- 4
- 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
- SEP, PO3
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 229 | 43% helix, 15% strand | Q63XU7 |
| C, D | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 230 | 43% helix, 15% strand | Q63XU7 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 4 copies · chains A, B, C, D
- PO3 · Phosphite ion · ion · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 6 copies · chains A, B, C, D
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 | 120 | 0.54 | 0.83 | 25 | PO3, SEP |
| 2 | 115 | 0.54 | 0.83 | 25 | PO3, SEP |
| 3 | 112 | 0.52 | 0.82 | 24 | PO3, SEP |
| 4 | 106 | 0.51 | 0.82 | 23 | PO3, SEP |
| 5 | 93 | 0.40 | 0.77 | 12 | empty |
Interfaces
2 interfaces between chains.
- B–C · 857 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GP3 · Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q63XU7 · AlphaFold monomer V2.0 prediction for 2,3-bisphosphoglycerate- dependent phosphoglycerate… · 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 Q63XU7
- Elsewhere: RCSB PDB 3GP3 · PDBe 3GP3 · UniProt Q63XU7
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