Research workbench
Structural basis of a point mutation that causes the genetic disease aspartylglucosaminuria
Analyse Structural basis of a point mutation that causes the genetic disease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R4Y
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase
- EC
- 3.5.1.26
- UniProt
- Q47898
- Ligands
- SD4
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase (EC 3.5.1.26) | protein | 293 | 35% helix, 24% strand | Q47898 |
| B | N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase (EC 3.5.1.26) | protein | 271 | 35% helix, 26% strand | Q47898 |
Ligands and binding sites
- SD4 · N-hydroxy-L-asparagine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.56 | 0.89 | 22 | empty |
| 2 | 158 | 0.47 | 0.77 | 18 | empty |
| 3 | 155 | 0.45 | 0.76 | 32 | empty |
| 4 | 112 | 0.40 | 0.76 | 23 | empty |
| 5 | 65 | 0.36 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2075 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4R4Y · Structural basis of a point mutation that causes the genetic disease… · the same entry in another collection · chain A against A, TM-score 1.00
- Q47898 · AlphaFold monomer V2.0 prediction for N(4)-(beta-N- acetylglucosaminyl)-L-asparaginase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q47898
- Elsewhere: RCSB PDB 4R4Y · PDBe 4R4Y · UniProt Q47898
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