Structure of PDB 1ybq Chain A

Receptor sequence

>1ybqA (length=389) Species: 562 (Escherichia coli)

MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNC
TVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSV
VGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEK
DVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVF
HMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGT
IDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSNGNGSQPFFDDEGNLT
HIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILP
GNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET

3D structure

• PDB: 1ybq Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli.
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H68 H70 K162 H201 H230 N285
• Catalytic site (residue number reindexed from 1): H68 H70 K162 H201 H230 N285
• Enzyme Commision number: 3.4.19.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	A	H68 H70 N285	H68 H70 N285
BS02	ZN	A	H201 H230	H201 H230
BS03	BDH	A	G74 G75 E77 T106 Y137 R169 R233 S289	G74 G75 E77 T106 Y137 R169 R233 S289

Gene Ontology

Molecular Function

• GO:0008237 metallopeptidase activity
• GO:0008270 zinc ion binding
• GO:0008798 beta-aspartyl-peptidase activity
• GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1ybq, PDBe:1ybq, PDBj:1ybq
• PDBsum: 1ybq
• PubMed: 15882050
• UniProt: P39377|IADA_ECOLI Isoaspartyl dipeptidase (Gene Name=iadA)