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Human aspartylglucosaminidase complex with reaction product
Analyse Human aspartylglucosaminidase complex with reaction product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1APZ
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartylglucosaminidase
- EC
- 3.5.1.26
- UniProt
- P20933
- Ligands
- ASP, NAG, BMA
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aspartylglucosaminidase (EC 3.5.1.26) | protein | 161 | 38% helix, 19% strand | P20933 |
| B, D | Aspartylglucosaminidase (EC 3.5.1.26) | protein | 141 | 20% helix, 41% strand | P20933 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains D, A, B, C
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.47 | 0.80 | 17 | empty |
| 2 | 117 | 0.44 | 0.78 | 23 | ASP |
| 3 | 110 | 0.43 | 0.78 | 23 | ASP |
| 4 | 102 | 0.42 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2819 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2813 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 1090 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 665 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 625 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1APZ · Human aspartylglucosaminidase complex with reaction product · the same entry in another collection · chain D against D, TM-score 1.00
- P20933 · 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 P20933
- Elsewhere: RCSB PDB 1APZ · PDBe 1APZ · UniProt P20933
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