Research workbench
Human glyoxalase I with an N-hydroxypyridone inhibitor
Analyse Human glyoxalase I with an N-hydroxypyridone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VW9
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoylglutathione lyase
- EC
- 4.4.1.5
- UniProt
- Q04760
- Ligands
- HPJ, ZN
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactoylglutathione lyase (EC 4.4.1.5) | protein | 176 | 28% helix, 28% strand | Q04760 |
Ligands and binding sites
- HPJ · 1-hydroxy-6-[1-(3-methoxypropyl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-4-phenylpyridin-2(1H)-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.67 | 0.81 | 36 | HPJ |
| 2 | 221 | 0.65 | 0.83 | 32 | HPJ |
| 3 | 146 | 0.42 | 0.75 | 26 | empty |
| 4 | 125 | 0.42 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 3689 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
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 Q04760
- Elsewhere: RCSB PDB 3VW9 · PDBe 3VW9 · UniProt Q04760
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