MolNFT v1 · #178651 · protein
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with udp-N-acetylglucosamine
7JHL · N-acetyllactosaminide beta-1,3-N…: “Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with udp-N-acetylglucosamine”. X-ray diffraction, 6 ligands (UD1, NAG, MAN), 8 pockets (best druggability 0.68). MolNFT v1 #178651 on…
- PDB
- 7JHL
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2
- EC
- 2.4.1.149
- UniProt
- Q9NY97
- Ligands
- UD1, NAG, MAN, BMA, MG, CL
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 331 | 41% helix, 18% strand | Q9NY97 |
| B | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 330 | 40% helix, 18% strand | Q9NY97 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.68 | 0.79 | 52 | NAG, UD1, MG |
| 2 | 317 | 0.61 | 0.78 | 38 | UD1, MG |
| 3 | 120 | 0.48 | 0.79 | 20 | NAG, PGE |
| 4 | 66 | 0.35 | 0.77 | 15 | empty |
| 5 | 70 | 0.34 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7JHL · Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP-N-acetylglucosamine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NY97 · AlphaFold monomer V2.0 prediction for N-acetyllactosaminide… · 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 Q9NY97
- Elsewhere: RCSB PDB 7JHL · PDBe 7JHL · UniProt Q9NY97
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