MolNFT v1 · #136816 · protein
Crystal structure of human GGT1 in complex with don
5V4Q · Gamma-glutamyltranspeptidase 1 heavy chain: “Crystal structure of human GGT1 in complex with don”. X-ray diffraction, 4 ligands (8WY, NAG, NA), 5 pockets (best druggability 0.74). MolNFT v1 #136816 on GenesisL1: 3D structure…
- PDB
- 5V4Q
- Type
- protein
- Length
- 532 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
- 8WY, NAG, NA, CL
- Pockets
- 5 · best druggability 0.74
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 | 343 | 50% 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 | 20% helix, 29% strand | P19440 |
Ligands and binding sites
- 8WY · 5,5-dihydroxy-L-norleucine · 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 | 603 | 0.74 | 0.81 | 69 | 8WY, CL |
| 2 | 76 | 0.35 | 0.76 | 18 | empty |
| 3 | 68 | 0.34 | 0.76 | 20 | empty |
| 4 | 59 | 0.33 | 0.77 | 16 | empty |
| 5 | 58 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 6210 Ų buried · 100 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
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 P19440
- Elsewhere: RCSB PDB 5V4Q · PDBe 5V4Q · UniProt P19440
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