MolNFT v1 · #92616 · protein
Crystal structure of human gamma-glutamyl transpeptidase--glutamate complex
4GDX · Gamma-glutamyltranspeptidase 1 heavy chain: “Crystal structure of human gamma-glutamyl transpeptidase--glutamate complex”. X-ray diffraction, 4 ligands (GLU, NAG, NA), 5 pockets (best druggability 0.76). MolNFT v1 #92616 on…
- PDB
- 4GDX
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltranspeptidase 1 heavy chain; Gamma-glutamyltranspeptidase 1 light chain
- EC
- 2.3.2.2, 3.4.19.13, 3.4.19.14
- UniProt
- P19440
- Ligands
- GLU, NAG, NA, CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyltranspeptidase 1 heavy chain (EC 2.3.2.2, 3.4.19.13, 3.4.19.14) | protein | 342 | 51% helix, 13% strand | P19440 |
| B | Gamma-glutamyltranspeptidase 1 light chain (EC 2.3.2.2, 3.4.19.13, 3.4.19.14) | protein | 189 | 19% helix, 28% strand | P19440 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.76 | 0.83 | 66 | GLU |
| 2 | 83 | 0.36 | 0.76 | 19 | empty |
| 3 | 61 | 0.36 | 0.78 | 20 | empty |
| 4 | 71 | 0.35 | 0.76 | 20 | empty |
| 5 | 57 | 0.30 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 6189 Ų buried · 101 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4GDX · Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate complex · the same entry in another collection · chain B against B, 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 4GDX · PDBe 4GDX · UniProt P19440
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