MolNFT v1 · #168637 · protein
Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for gt-a glycosyltransferases
6WMN · 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, BMA), 12 pockets (best druggability 0.75).…
- PDB
- 6WMN
- Type
- protein
- Length
- 1,273 residues
- Chains
- 4
- 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, MAN, MG, CL
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 318 | 38% helix, 19% strand | Q9NY97 |
| B | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 326 | 40% helix, 19% strand | Q9NY97 |
| C | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 327 | 40% helix, 20% strand | Q9NY97 |
| D | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 302 | 37% helix, 21% strand | Q9NY97 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.75 | 0.79 | 109 | NAG, UDP, MG |
| 2 | 521 | 0.70 | 0.79 | 65 | MG, UDP |
| 3 | 259 | 0.60 | 0.80 | 37 | UDP |
| 4 | 318 | 0.54 | 0.75 | 24 | empty |
| 5 | 82 | 0.49 | 0.83 | 19 | NAG |
Interfaces
4 interfaces between chains.
- A–B · 1019 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1008 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 223 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 73 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6WMN · Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NY97 · AlphaFold monomer V2.0 prediction for N-acetyllactosaminide… · a predicted model of the same protein · chain B 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 6WMN · PDBe 6WMN · UniProt Q9NY97
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