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Crystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710B with bound 2,3-diphosphoglyceric acid and 3- phosphoglyceric acid
Analyse Crystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FDZ
- Type
- protein
- Length
- 459 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
- Q3JWH7
- Ligands
- DG2, 3PG
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 230 | 44% helix, 15% strand | Q3JWH7 |
| B | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 229 | 42% helix, 16% strand | Q3JWH7 |
Ligands and binding sites
- DG2 · (2R)-2,3-diphosphoglyceric acid · ligand · chains A
- 3PG · 3-phosphoglyceric acid · ligand · chains B
- PEG · Di(hydroxyethyl)ether · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.49 | 0.85 | 23 | DG2 |
| 2 | 72 | 0.46 | 0.83 | 23 | 3PG |
| 3 | 116 | 0.37 | 0.73 | 18 | empty |
| 4 | 65 | 0.35 | 0.77 | 10 | empty |
| 5 | 81 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 849 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3FDZ · Crystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710b with bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q3JWH7 · AlphaFold monomer V2.0 prediction for 2,3-bisphosphoglycerate- dependent phosphoglycerate… · a predicted model of the same protein · chain A 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 Q3JWH7
- Elsewhere: RCSB PDB 3FDZ · PDBe 3FDZ · UniProt Q3JWH7
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