MolNFT v1 · #17244 · protein
Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with udp and GLCUAB(1-3)GALB(1-O)-naphthalenelmethanol an acceptor substrate analog
1ON8 · Alpha-1,4-N-acetylhexosaminyltransferase EXTL2: “Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with udp and…”. X-ray diffraction, 4 ligands (UDP, GAL, BDP), 5 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 1ON8
- Type
- protein
- Length
- 527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
- EC
- 2.4.1.-
- UniProt
- Q9ES89
- Ligands
- UDP, GAL, BDP, MN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,4-N-acetylhexosaminyltransferase EXTL2 (EC 2.4.1.-) | protein | 265 | 31% helix, 25% strand | Q9ES89 |
| B | Alpha-1,4-N-acetylhexosaminyltransferase EXTL2 (EC 2.4.1.-) | protein | 262 | 30% helix, 24% strand | Q9ES89 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.74 | 0.83 | 52 | GAL, BDP, MN, UDP |
| 2 | 526 | 0.72 | 0.81 | 47 | GAL, BDP, MN, UDP |
| 3 | 104 | 0.51 | 0.81 | 23 | EDO |
| 4 | 89 | 0.34 | 0.74 | 16 | empty |
| 5 | 70 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1385 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1ON8 · Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with UDP and… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9ES89 · AlphaFold monomer V2.0 prediction for exostosin-like 2 (Q9ES89) · 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 Q9ES89
- Elsewhere: RCSB PDB 1ON8 · PDBe 1ON8 · UniProt Q9ES89
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