MolNFT v1 · #163406 · protein
Crystal structure of the tggalnac-T3 in complex with udp, manganese and the peptide 3
6S24 · Polypeptide N-acetylgalactosaminyltransferase: “Crystal structure of the tggalnac-T3 in complex with udp, manganese and the peptide 3”. X-ray diffraction, 6 ligands (TAM, UDP, NAG), 4 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6S24
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase…
- EC
- 2.4.1.-
- UniProt
- H0ZAB5
- Ligands
- TAM, UDP, NAG, NGA, MN, PO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.-) | protein | 537 | 29% helix, 23% strand | H0ZAB5 |
| F | Ala-thr-gly-ala-gly-ala-gly-ala-gly-thr-thr-pro-gly-pro | protein | 14 | 0% helix, 0% strand | — |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A, F
- UDP · Uridine-5'-diphosphate · ligand · chains A, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A, F
- MN · Manganese (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · 16 copies · chains A, F
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 | 871 | 0.82 | 0.84 | 97 | TAM, UDP, MN |
| 2 | 142 | 0.53 | 0.80 | 25 | PO4 |
| 3 | 182 | 0.46 | 0.74 | 24 | empty |
| 4 | 68 | 0.41 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–F · 691 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 6S24 · Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3 · the same entry in another collection · chain A against A, TM-score 1.00
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 H0ZAB5
- Elsewhere: RCSB PDB 6S24 · PDBe 6S24 · UniProt H0ZAB5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.