MolNFT v1 · #180794 · protein
Structure of human GGT1 in complex with LNT2-65 compound
7LBC · Glutathione hydrolase 1 heavy chain: “Structure of human GGT1 in complex with LNT2-65 compound”. X-ray diffraction, 4 ligands (XSA, NAG, CL), 4 pockets (best druggability 0.75). MolNFT v1 #180794 on GenesisL1: 3D structure, binding…
- PDB
- 7LBC
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione hydrolase 1 heavy chain; Glutathione hydrolase 1 light chain
- EC
- 3.4.19.13, 2.3.2.2, 3.4.19.14
- UniProt
- P19440
- Ligands
- XSA, NAG, CL, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione hydrolase 1 heavy chain (EC 3.4.19.13, 2.3.2.2, 3.4.19.14) | protein | 342 | 51% helix, 12% strand | P19440 |
| B | Glutathione hydrolase 1 light chain (EC 3.4.19.13, 2.3.2.2, 3.4.19.14) | protein | 187 | 19% helix, 28% strand | P19440 |
Ligands and binding sites
- XSA · (2R)-2-[(2-aminoethyl)amino]-4-boronobutanoic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.75 | 0.83 | 65 | XSA, SO4 |
| 2 | 112 | 0.40 | 0.76 | 21 | empty |
| 3 | 80 | 0.36 | 0.76 | 19 | empty |
| 4 | 60 | 0.34 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 6215 Ų buried · 99 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 7LBC · Structure of human GGT1 in complex with Lnt2-65 compound · the same entry in another collection · chain A against A, TM-score 1.00
- P19440 · AlphaFold monomer V2.0 prediction for glutathione hydrolase 1 proenzyme (P19440) · a predicted model of the same protein · chain A 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 P19440
- Elsewhere: RCSB PDB 7LBC · PDBe 7LBC · UniProt P19440
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