Structure of PDB 3ly0 Chain B Binding Site BS03

Receptor Information

>3ly0 Chain B (length=352) Species: 272943 (Cereibacter sphaeroides 2.4.1)

DTIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGF
FAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLL
WMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLF
HSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRL
KIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMI
RESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMG
SDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERT
WG

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 3ly0 Chain B Residue 365

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ly0 Crystal structure of metallo peptidase from Rhodobacter sphaeroides liganded with phosphinate mimic of dipeptide L-Ala-D-Ala
• Resolution: 1.399 Å
• Binding residue (original residue number in PDB): E137 H210 H231
• Binding residue (residue number reindexed from 1): E135 H208 H229
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H11 D13 E137 W164 H210 H231 D304
• Catalytic site (residue number reindexed from 1): H9 D11 E135 W162 H208 H229 D302
• Enzyme Commision number: 3.4.13.19: membrane dipeptidase.

Gene Ontology

Molecular Function

• GO:0016805 dipeptidase activity
• GO:0046872 metal ion binding
• GO:0070573 metallodipeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3ly0, PDBe:3ly0, PDBj:3ly0
• PDBsum: 3ly0
• UniProt: Q3IZQ3