Research workbench
Crystal structure of pp-galnac-T10 with udp, galnac and MN2+
Analyse Crystal structure of pp-galnac-T10 with udp, galnac and MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D7I
- 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, NAG, NGA, MN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 10 (EC 2.4.1.41) | protein | 536 | 26% helix, 21% strand | Q86SR1 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- NGA · 2-acetamido-2-deoxy-beta-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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.71 | 0.82 | 39 | NGA, MN, UDP |
| 2 | 143 | 0.51 | 0.80 | 32 | empty |
| 3 | 162 | 0.50 | 0.78 | 23 | empty |
| 4 | 80 | 0.36 | 0.76 | 16 | empty |
| 5 | 54 | 0.35 | 0.79 | 12 | empty |
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2D7I · Crystal structure of pp-GalNAc-T10 with UDP, GalNAc and Mn2+ · 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 2D7I · PDBe 2D7I · UniProt Q86SR1
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