MolNFT v1 · #147550 · protein
Crystal structure of the galnac-T2 F104S mutant in complex with udp- galnac
6EGS · Polypeptide N-acetylgalactosaminyltransferase 2: “Crystal structure of the galnac-T2 F104S mutant in complex with udp- galnac”. X-ray diffraction, 2 ligands (UD2, MN), 9 pockets (best druggability 0.83). MolNFT v1 #147550 on…
- PDB
- 6EGS
- Type
- protein
- Length
- 945 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase 2
- EC
- 2.4.1.41
- UniProt
- Q10471
- Ligands
- UD2, MN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 478 | 28% helix, 26% strand | Q10471 |
| B | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 467 | 30% helix, 27% strand | Q10471 |
Ligands and binding sites
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.83 | 0.84 | 90 | empty |
| 2 | 510 | 0.68 | 0.78 | 54 | MN, UD2 |
| 3 | 502 | 0.67 | 0.78 | 56 | UD2 |
| 4 | 403 | 0.63 | 0.78 | 48 | empty |
| 5 | 80 | 0.53 | 0.85 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1757 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6EGS · Crystal structure of the GalNAc-T2 F104S mutant in complex with UDP-GalNAc · the same entry in another collection · chain A against A, TM-score 1.00
- Q10471 · AlphaFold monomer V2.0 prediction for polypeptide N-acetylgalactosaminyltransferase 2… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q10471
- Elsewhere: RCSB PDB 6EGS · PDBe 6EGS · UniProt Q10471
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