MolNFT v1 · #168636 · protein
Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for gt-a glycosyltransferases
6WMM · N-acetyllactosaminide beta-1,3-N…: “Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for…”. X-ray diffraction, 4 ligands (UDP, NAG, BMA), 3 pockets (best druggability 0.71).…
- PDB
- 6WMM
- Type
- protein
- Length
- 648 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, BMA, MG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 321 | 39% helix, 19% strand | Q9NY97 |
| B | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 327 | 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 · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.71 | 0.79 | 76 | NAG, EPE, UDP |
| 2 | 361 | 0.66 | 0.80 | 54 | NAG, UDP |
| 3 | 60 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 5 disulfide, 4 glycan (engineered, disulfide, N-glycosylation).
Compared structures
- 6WMM · 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 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 Q9NY97
- Elsewhere: RCSB PDB 6WMM · PDBe 6WMM · UniProt Q9NY97
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