MolNFT v1 · #48791 · protein
Ensemble refinement of the protein crystal structure of glyoxalase II from arabidopsis thaliana gene AT2G31350
2Q42 · Putative hydroxyacylglutathione hydrolase 2: “Ensemble refinement of the protein crystal structure of glyoxalase II from arabidopsis thaliana gene AT2G31350”. X-ray diffraction, 2 ligands (ZN, FE), 2 pockets (best druggability…
- PDB
- 2Q42
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydroxyacylglutathione hydrolase 2
- EC
- 3.1.2.6
- UniProt
- Q9SID3
- Ligands
- ZN, FE
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative hydroxyacylglutathione hydrolase 2 (EC 3.1.2.6) | protein | 254 | 35% helix, 24% strand | Q9SID3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.85 | 0.87 | 69 | ACY |
| 2 | 172 | 0.47 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 793 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2Q42 · Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SID3 · AlphaFold monomer V2.0 prediction for hydroxyacylglutathione hydrolase 2, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9SID3
- Elsewhere: RCSB PDB 2Q42 · PDBe 2Q42 · UniProt Q9SID3
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