Research workbench
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 in unliganded form
Analyse Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 in unliganded form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JHK
- Type
- protein
- Length
- 1,315 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
- NAG, BMA, MAN, NA, CL
- Pockets
- 19 · best druggability 0.66
Structure
x-ray diffraction · 3 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 | 323 | 40% helix, 18% strand | Q9NY97 |
| B, C | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 331 | 41% helix, 19% strand | Q9NY97 |
| D | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 330 | 41% helix, 17% strand | Q9NY97 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, D
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.66 | 0.77 | 59 | empty |
| 2 | 387 | 0.61 | 0.77 | 43 | empty |
| 3 | 251 | 0.55 | 0.77 | 33 | empty |
| 4 | 262 | 0.54 | 0.76 | 32 | CL |
| 5 | 248 | 0.52 | 0.76 | 30 | NA |
Interfaces
3 interfaces between chains.
- A–B · 989 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 556 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7JHK · Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 in unliganded form · 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 7JHK · PDBe 7JHK · UniProt Q9NY97
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