Research workbench
Human glyoxalase II with cacodylate and acetate ions present in the active site
Analyse Human glyoxalase II with cacodylate and acetate ions present in the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QH3
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hydroxyacylglutathione hydrolase)
- EC
- 3.1.2.6
- UniProt
- Q16775
- Ligands
- ZN, MN, CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (hydroxyacylglutathione hydrolase) (EC 3.1.2.6) | protein | 260 | 33% helix, 25% strand | Q16775 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- CAC · Cacodylate ion · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.60 | 0.78 | 26 | CL |
| 2 | 110 | 0.38 | 0.74 | 22 | CAC, ACT |
| 3 | 95 | 0.37 | 0.75 | 19 | CAC, ACT |
Interfaces
1 interface between chains.
- A–B · 331 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1QH3 · Human glyoxalase II with cacodylate and acetate ions present in the active site · the same entry in another collection · chain A against A, TM-score 1.00
- Q16775 · AlphaFold monomer V2.0 prediction for hydroxyacylglutathione hydrolase, 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 Q16775
- Elsewhere: RCSB PDB 1QH3 · PDBe 1QH3 · UniProt Q16775
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