Research workbench
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 iodide- derivative
Analyse Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 iodide- derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JHI
- Type
- protein
- Length
- 1,311 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, IOD, CL
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 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 | 330 | 40% helix, 19% strand | Q9NY97 |
| B | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 328 | 40% helix, 19% strand | Q9NY97 |
| C | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 331 | 38% helix, 19% strand | Q9NY97 |
| D | N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase 2 (EC 2.4.1.149) | protein | 322 | 39% helix, 20% strand | Q9NY97 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, C, D
- MAN · alpha-D-mannopyranose · sugar · chains C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- IOD · Iodide ion · ion · 41 copies · chains A, C, B, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.73 | 0.77 | 96 | MG, UDP, IOD |
| 2 | 393 | 0.65 | 0.79 | 52 | NAG, UDP |
| 3 | 271 | 0.57 | 0.78 | 30 | IOD |
| 4 | 243 | 0.53 | 0.77 | 34 | MG |
| 5 | 253 | 0.52 | 0.75 | 34 | IOD |
Interfaces
3 interfaces between chains.
- A–D · 1015 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 566 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7JHI · Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 iodide-derivative · 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 7JHI · PDBe 7JHI · UniProt Q9NY97
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