Research workbench
The complex structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase RV2419C with inorganic phosphate
Analyse The complex structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PZA
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosyl-3-phosphoglycerate phosphatase
- EC
- 3.1.3.-, 3.1.3.70
- UniProt
- P9WIC6
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.-, 3.1.3.70) | protein | 207 | 41% helix, 19% strand | P9WIC6 |
| B | Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.-, 3.1.3.70) | protein | 217 | 41% helix, 18% strand | P9WIC6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.64 | 0.79 | 40 | PO4 |
| 2 | 300 | 0.60 | 0.79 | 31 | PO4 |
| 3 | 167 | 0.44 | 0.75 | 32 | empty |
| 4 | 59 | 0.39 | 0.80 | 15 | empty |
| 5 | 80 | 0.37 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 884 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4PZA · The complex structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase Rv2419c… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WIC6 · AlphaFold monomer V2.0 prediction for glucosyl-3-phosphoglycerate phosphatase (P9WIC6) · 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 P9WIC6
- Elsewhere: RCSB PDB 4PZA · PDBe 4PZA · UniProt P9WIC6
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