Structure of PDB 5xev Chain A Binding Site BS02

Receptor Information

>5xev Chain A (length=409) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

STPIPAMQAALAATDLDGWLVYDFQGLNPHARRVLGIGDDVFLTRRFFVW
VPRAGRAVVLHNHIEGGNWNRITQEWDAELRPFGSHAELDAALRGVVSGQ
RLAMEYSPNGAVPYVSRVDAGTLERVRGAGAAEVASSADLLQAFLVWTPD
DLAAHRRAAALLMRAKDDAFRLIHDRLRAGQSVTEWEVQQLIMDQIRAAG
MQAGHDVNVSFGVNAADSHYEPSEQRSATLHPGECVLIDLWAQEPGRPFA
DVTWVGFAGEPGTEYLDAWQAVRAAREAALELLRSRFVAEGYGRLQGWEL
DRAARDAMGERWAPHFLHRTGHDLGVQIHGAGANLDDYETRDTRTLTPGL
SVTVEPGTYPAAGGFGIRSEVDVYLAPDGPEVTTDLQQAPFILGVGDWDA
VRAAGYGEQ

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: 5xev Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xev Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): D240 D252 E377
• Binding residue (residue number reindexed from 1): D239 D251 E370
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H220 D240 A251 H319 H323 H330 T354 G358 R375 E377
• Catalytic site (residue number reindexed from 1): H219 D239 A250 H318 H322 H329 T353 G357 R368 E370
• Enzyme Commision number: 3.4.13.9: Xaa-Pro dipeptidase.

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:5xev, PDBe:5xev, PDBj:5xev
• PDBsum: 5xev
• PubMed: 28929533
• UniProt: Q9RX37