Research workbench
Crystal structure of the active form of galnac-T2 in complex with udp and the glycopeptide MUC5AC-13
Analyse Crystal structure of the active form of galnac-T2 in complex with udp and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AJP
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase 2; Mucin
- EC
- 2.4.1.41
- UniProt
- Q10471, Q14886
- Ligands
- UDP, A2G, MN, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 495 | 31% helix, 24% strand | Q10471 |
| B | Mucin | protein | 14 | 0% helix, 0% strand | Q14886 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A, B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A, B
- MN · Manganese (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 21 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.80 | 0.83 | 113 | UDP, MN, A2G |
| 2 | 85 | 0.41 | 0.78 | 15 | empty |
| 3 | 95 | 0.40 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 811 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 5AJP · Crystal structure of the active form of GalNAc-T2 in complex with UDP and the… · 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 A against A, TM-score 0.99
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
- Every structure of UniProt Q14886
- Elsewhere: RCSB PDB 5AJP · PDBe 5AJP · UniProt Q10471 · UniProt Q14886
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