MolNFT v1 · #168638 · protein
Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for gt-a glycosyltransferases
6WMO · N-acetyllactosaminide beta-1,3-N…: “Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for…”. X-ray diffraction, 6 ligands (UDP, NAG, GAL), 4 pockets (best druggability 0.77).…
- PDB
- 6WMO
- Type
- protein
- Length
- 638 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
- UDP, NAG, GAL, BMA, MAN, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% 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 | 325 | 40% helix, 18% strand | Q9NY97 |
| B | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 313 | 39% helix, 19% strand | Q9NY97 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · chains B
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 | 926 | 0.77 | 0.79 | 100 | GAL, NAG, MG, UDP, EDO, GOL |
| 2 | 89 | 0.49 | 0.82 | 17 | NAG |
| 3 | 66 | 0.31 | 0.74 | 13 | empty |
| 4 | 52 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 984 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6WMO · Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of… · 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 6WMO · PDBe 6WMO · UniProt Q9NY97
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