MolNFT v1 · #49023 · protein
Saccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate complex
2QB7: “Saccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate complex”. X-ray diffraction, 2 ligands (CO, PO4), 10 pockets (best druggability 0.83). MolNFT v1 #49023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QB7
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exopolyphosphatase
- EC
- 3.6.1.11
- UniProt
- P38698
- Ligands
- CO, PO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exopolyphosphatase (EC 3.6.1.11) | protein | 393 | 48% helix, 19% strand | P38698 |
| B | Exopolyphosphatase (EC 3.6.1.11) | protein | 389 | 47% helix, 19% strand | P38698 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.83 | 0.85 | 69 | CO, PO4, ACT |
| 2 | 760 | 0.80 | 0.84 | 69 | CO, PO4, EDO |
| 3 | 335 | 0.72 | 0.84 | 56 | EDO |
| 4 | 202 | 0.64 | 0.84 | 30 | empty |
| 5 | 102 | 0.44 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1245 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2QB7 · Saccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate complex · the same entry in another collection · chain A against A, TM-score 1.00
- P38698 · AlphaFold monomer V2.0 prediction for exopolyphosphatase (P38698) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P38698
- Elsewhere: RCSB PDB 2QB7 · PDBe 2QB7 · UniProt P38698
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