Research workbench
Crystal structure of escherichia COLI isoaspartyl dipeptidase mutant D285N complexed with beta-aspartylhistidine
Analyse Crystal structure of escherichia COLI isoaspartyl dipeptidase mutant D285N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YBQ
- 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
- BDH, ZN
- Pockets
- 3 · best druggability 0.67
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
- BDH · L-beta-aspartylhistidine · ligand · 2 copies · chains A, B
- 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.67 | 0.86 | 36 | ZN, BDH |
| 2 | 199 | 0.64 | 0.84 | 36 | BDH |
| 3 | 388 | 0.54 | 0.73 | 58 | empty |
Interfaces
1 interface between chains.
- A–B · 1079 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 1YBQ · Crystal structure of Escherichia coli isoaspartyl dipeptidase mutant D285N 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 A 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 1YBQ · PDBe 1YBQ · UniProt P39377
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