Research workbench
Crystal structure of isoaspartyl dipeptidase from E. COLI
Analyse Crystal structure of isoaspartyl dipeptidase from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ONW
- Type
- protein
- Length
- 756 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
- ZN, MG, NA, CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 376 | 31% helix, 26% strand | P39377 |
| B | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 380 | 31% helix, 26% strand | P39377 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.60 | 0.73 | 61 | EDO |
| 2 | 191 | 0.54 | 0.79 | 27 | empty |
| 3 | 122 | 0.48 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1102 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
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 1ONW · PDBe 1ONW · UniProt P39377
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