MolNFT v1 · #34161 · protein
Crystal structure of pp-galnac-T10 complexed with galnac-ser on lectin domain
2D7R · Polypeptide N-acetylgalactosaminyltransferase 10: “Crystal structure of pp-galnac-T10 complexed with galnac-ser on lectin domain”. X-ray diffraction, 6 ligands (UDP, SER, NAG), 4 pockets (best druggability 0.76). MolNFT v1 #34161 on…
- PDB
- 2D7R
- Type
- protein
- Length
- 536 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase 10
- EC
- 2.4.1.41
- UniProt
- Q86SR1
- Ligands
- UDP, SER, NAG, NGA, A2G, MN
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 10 (EC 2.4.1.41) | protein | 536 | 25% helix, 21% strand | Q86SR1 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- SER · Serine · ligand
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
- MN · Manganese (II) ion · metal · chains A
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 | 559 | 0.76 | 0.83 | 67 | NGA, UDP |
| 2 | 129 | 0.53 | 0.81 | 29 | empty |
| 3 | 140 | 0.46 | 0.77 | 20 | empty |
| 4 | 91 | 0.42 | 0.78 | 25 | empty |
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2D7R · Crystal structure of pp-GalNAc-T10 complexed with GalNAc-Ser on lectin domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q86SR1 · AlphaFold monomer V2.0 prediction for polypeptide N-acetylgalactosaminyltransferase 10… · a predicted model of the same protein · 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 Q86SR1
- Elsewhere: RCSB PDB 2D7R · PDBe 2D7R · UniProt Q86SR1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.