MolNFT v1 · #55887 · protein
Crystal structure of the phosphoglycolate phosphatase from aquifex aeolicus VF5
2YY6: “Crystal structure of the phosphoglycolate phosphatase from aquifex aeolicus VF5”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.72). MolNFT v1 #55887 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YY6
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycolate phosphatase
- EC
- 3.1.3.18
- UniProt
- O67359
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoglycolate phosphatase (EC 3.1.3.18) | protein | 208 | 45% helix, 13% strand | O67359 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.72 | 0.82 | 49 | empty |
| 2 | 231 | 0.64 | 0.83 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2YY6 · Crystal Structure of the phosphoglycolate phosphatase from Aquifex aeolicus VF5 · the same entry in another collection · chain A against A, TM-score 1.00
- O67359 · AlphaFold monomer V2.0 prediction for phosphoglycolate phosphatase (O67359) · 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 O67359
- Elsewhere: RCSB PDB 2YY6 · PDBe 2YY6 · UniProt O67359
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