Research workbench
Ensemble refinement of the protein crystal structure of an aspartoacylase from rattus norvegicus
Analyse Ensemble refinement of the protein crystal structure of an aspartoacylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q4Z
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartoacylase
- EC
- 3.5.1.15
- UniProt
- Q9R1T5
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartoacylase (EC 3.5.1.15) | protein | 307 | 28% helix, 24% strand | Q9R1T5 |
Ligands and binding sites
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 | 211 | 0.75 | 0.90 | 32 | ZN |
| 2 | 398 | 0.75 | 0.85 | 48 | SO4 |
| 3 | 834 | 0.73 | 0.78 | 63 | SO4 |
| 4 | 132 | 0.47 | 0.79 | 23 | empty |
| 5 | 97 | 0.37 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1210 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2Q4Z · Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R1T5 · AlphaFold monomer V2.0 prediction for aspartoacylase (Q9R1T5) · 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 Q9R1T5
- Elsewhere: RCSB PDB 2Q4Z · PDBe 2Q4Z · UniProt Q9R1T5
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