Research workbench
Human glyoxalase I complexed with S-P- nitrobenzyloxycarbonylglutathione
Analyse Human glyoxalase I complexed with S-P- nitrobenzyloxycarbonylglutathione in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QIP
- Type
- protein
- Length
- 718 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (lactoylglutathione lyase)
- EC
- 4.4.1.5
- UniProt
- Q04760
- Ligands
- GNB, ZN
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (lactoylglutathione lyase) (EC 4.4.1.5) | protein | 176 | 27% helix, 30% strand | Q04760 |
| B, D | Protein (lactoylglutathione lyase) (EC 4.4.1.5) | protein | 183 | 26% helix, 28% strand | Q04760 |
Ligands and binding sites
- GNB · S-P-nitrobenzyloxycarbonylglutathione · ligand · 4 copies · chains A, B, D, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.86 | 0.87 | 91 | GNB, BME |
| 2 | 358 | 0.66 | 0.79 | 41 | GNB, BME |
| 3 | 356 | 0.64 | 0.79 | 37 | GNB, BME |
| 4 | 127 | 0.47 | 0.78 | 24 | empty |
| 5 | 153 | 0.41 | 0.74 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3708 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3696 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 328 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 169 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 129 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 1QIP · Human glyoxalase I complexed with S-P-nitrobenzyloxycarbonylglutathione · the same entry in another collection · chain C against C, TM-score 1.00
- Q04760 · AlphaFold monomer V2.0 prediction for lactoylglutathione lyase (Q04760) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 1QIP · PDBe 1QIP · UniProt Q04760
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