Structure of PDB 5cdl Chain A Binding Site BS01

Receptor Information

>5cdl Chain A (length=349) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

SSKMDQLRPVLGRAGVDALWVSAPANVRWLSGFTSAEDGKVLVSPDGATL
YTDARYTVQAQEESSLPQYIARPPATYEHAADTVRGLRVGFEAESLTVAE
LEDLRQAWPNSTLVALRGTLGGLRAVKTPEEIGAIRAAQDLADRVYTEVR
PMIRAGVRELDVAVEIETRLRRAGGESAFELIVASGPNGAKPHGHASKRV
IEDGDLVTIDMGARLGGYNSDMTRTVAVGTPSAEMKRVYDAVLEAEEAAI
AAIRPGVRAADLDKLARDLLTRHGLGEAFAHSLGHGVGLEVHEGPGLRGT
SQDVLEAGMVITIEPGAYLPGVGGVRIEDLILVTEDGYEVLSHSAKESV

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 5cdl Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5cdl Proline dipeptidase from Deinococcus radiodurans (selenomethionine derivative)
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): D210 D221 M222 T223 E328
• Binding residue (residue number reindexed from 1): D210 D221 M222 T223 E328
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D82 H193 D210 D221 T223 H281 H285 H292 E314 Y318 R326 E328
• Catalytic site (residue number reindexed from 1): D82 H193 D210 D221 T223 H281 H285 H292 E314 Y318 R326 E328

Gene Ontology

Molecular Function

• GO:0004177 aminopeptidase activity
• GO:0008235 metalloexopeptidase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding
• GO:0046914 transition metal ion binding

External links

• PDB: RCSB:5cdl, PDBe:5cdl, PDBj:5cdl
• PDBsum: 5cdl
• UniProt: Q9RUY4