MolNFT v1 · #128006 · protein
Small-molecule inhibition of ppgalnac-ts selectively reduces mucin- type O-glycosylation
5NDF · Polypeptide N-acetylgalactosaminyltransferase 2: “Small-molecule inhibition of ppgalnac-ts selectively reduces mucin- type O-glycosylation”. X-ray diffraction, 3 ligands (UDP, LU2, MN), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5NDF
- Type
- protein
- Length
- 2,967 residues
- Chains
- 6
- 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
- UDP, LU2, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 495 | 29% helix, 25% strand | Q10471 |
| E | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 492 | 29% helix, 24% strand | Q10471 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- LU2 · 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one · ligand · 3 copies · chains A, B, D
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.82 | 0.84 | 93 | empty |
| 2 | 627 | 0.76 | 0.82 | 57 | MN, UDP, EDO, LU2 |
| 3 | 613 | 0.75 | 0.82 | 61 | MN, UDP, EDO, LU2 |
| 4 | 353 | 0.74 | 0.85 | 41 | MN, UDP |
| 5 | 368 | 0.74 | 0.85 | 43 | UDP |
Interfaces
8 interfaces between chains.
- A–B · 1584 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 444 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 335 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 279 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 5NDF · Small-molecule inhibition of ppGalNAc-Ts selectively reduces mucin-type O-glycosylation · the same entry in another collection · chain F against F, TM-score 1.00
- Q10471 · AlphaFold monomer V2.0 prediction for polypeptide N-acetylgalactosaminyltransferase 2… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5NDF · PDBe 5NDF · UniProt Q10471
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