MolNFT v1 · #169545 · protein
Crystal structures of beta-1,4-N-acetylglucosaminyltransferase 2 (POMGNT2): structural basis for inherited muscular dystrophies
6XFI · Protein O-linked-mannose beta-1,4-N…: “Crystal structures of beta-1,4-N-acetylglucosaminyltransferase 2 (POMGNT2): structural basis for inherited…”. X-ray diffraction, 3 ligands (UDP, NAG, PO4), 4 pockets (best druggability 0.69).…
- PDB
- 6XFI
- Type
- protein
- Length
- 511 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2
- EC
- 2.4.1.312
- UniProt
- Q8NAT1
- Ligands
- UDP, NAG, PO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 511 | 28% helix, 27% strand | Q8NAT1 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- PO4 · Phosphate ion · ion · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.69 | 0.80 | 42 | UDP |
| 2 | 50 | 0.42 | 0.83 | 16 | empty |
| 3 | 120 | 0.41 | 0.76 | 16 | empty |
| 4 | 72 | 0.33 | 0.75 | 15 | PO4 |
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6XFI · Crystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2): Structural… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NAT1 · AlphaFold monomer V2.0 prediction for protein O-linked-mannose… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8NAT1
- Elsewhere: RCSB PDB 6XFI · PDBe 6XFI · UniProt Q8NAT1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.