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Crystal structure of mouse alpha-1,4-N-acetylhexosaminotransferase (EXTL2) in complex with udpglcnac
Analyse Crystal structure of mouse alpha-1,4-N-acetylhexosaminotransferase (EXTL2) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ON6
- Type
- protein
- Length
- 511 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
- UD1, MN
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,4-N-acetylhexosaminyltransferase EXTL2 (EC 2.4.1.-) | protein | 254 | 31% helix, 26% strand | Q9ES89 |
| B | Alpha-1,4-N-acetylhexosaminyltransferase EXTL2 (EC 2.4.1.-) | protein | 257 | 33% helix, 26% strand | Q9ES89 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.55 | 0.76 | 43 | UD1 |
| 2 | 245 | 0.52 | 0.76 | 29 | MN, UD1 |
| 3 | 106 | 0.49 | 0.80 | 22 | EDO |
| 4 | 57 | 0.36 | 0.78 | 20 | empty |
| 5 | 101 | 0.35 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1357 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1ON6 · Crystal structure of mouse alpha-1,4-N-acetylhexosaminotransferase (EXTL2) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ES89 · AlphaFold monomer V2.0 prediction for exostosin-like 2 (Q9ES89) · 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 Q9ES89
- Elsewhere: RCSB PDB 1ON6 · PDBe 1ON6 · UniProt Q9ES89
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