Research workbench
Ensemble refinement of the protein crystal structure of glyoxalase II from arabidopsis thaliana gene AT2G31350
Analyse Ensemble refinement of the protein crystal structure of glyoxalase II from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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