Research workbench
Crystal structure of isoaspartyl dipeptidase from escherichia COLI complexed with aspartate
Analyse Crystal structure of isoaspartyl dipeptidase from escherichia COLI complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ONX
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoaspartyl dipeptidase
- EC
- 3.4.19.-
- UniProt
- P39377
- Ligands
- ASP, ZN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 389 | 30% helix, 28% strand | P39377 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.65 | 0.85 | 34 | ZN, ASP |
| 2 | 201 | 0.61 | 0.82 | 38 | ASP |
| 3 | 230 | 0.46 | 0.73 | 29 | empty |
| 4 | 172 | 0.41 | 0.73 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1092 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 1ONX · Crystal structure of isoaspartyl dipeptidase from escherichia coli complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- P39377 · AlphaFold monomer V2.0 prediction for isoaspartyl dipeptidase (P39377) · 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 P39377
- Elsewhere: RCSB PDB 1ONX · PDBe 1ONX · UniProt P39377
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