Research workbench
Crystal structure of E. COLI isoaspartyl dipeptidase mutant Y137F
Analyse Crystal structure of E. COLI isoaspartyl dipeptidase mutant Y137F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AQV
- Type
- protein
- Length
- 750 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
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 375 | 31% helix, 26% strand | P39377 |
| B | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 375 | 32% helix, 26% strand | P39377 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
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 | 106 | 0.49 | 0.81 | 24 | empty |
| 2 | 150 | 0.48 | 0.78 | 29 | empty |
| 3 | 224 | 0.44 | 0.72 | 29 | empty |
| 4 | 197 | 0.44 | 0.73 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1089 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 2AQV · Crystal Structure of E. coli Isoaspartyl Dipeptidase mutant Y137F · the same entry in another collection · chain A against A, 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 1.00
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 2AQV · PDBe 2AQV · UniProt P39377
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