Structure of PDB 5dk5 Chain A Binding Site BS01

Receptor Information
>5dk5 Chain A (length=294) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HCPFDTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNK
YVKPVLNRTLTKNCVDFTGIPQRSIDTADTFDVVYEQFQQWLITLGLEEG
KFAFVCDSRQDLWRIAQYQMKLSNIQMPAFFRQYINLYKIFTNEMDRMGP
KELSATTNIGKMNEYYDLPTIGRAHDAMDDCLNIATILQRMINMGAKVTV
NELLTCCASWRRQPLVYNKEWRSSFMDAGKIFERVLPLVVTTIRAGDFRL
EMYGVCRYCRKGMDVCGTSHQQTPHDLYKNEEDPIHFAKIAGYY
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain5dk5 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5dk5 Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES)
Resolution2.1 Å
Binding residue
(original residue number in PDB)		C210 C260 C263 C270
Binding residue
(residue number reindexed from 1)		C206 C256 C259 C266
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D15 E17 D115 H179 D184
Catalytic site (residue number reindexed from 1) D11 E13 D111 H175 D180
Enzyme Commision number 3.1.-.-
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003676 nucleic acid binding
GO:0003697 single-stranded DNA binding
GO:0004520 DNA endonuclease activity
GO:0004527 exonuclease activity
GO:0004536 DNA nuclease activity
GO:0004540 RNA nuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0046872 metal ion binding
Biological Process
GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006308 DNA catabolic process
GO:0006309 apoptotic DNA fragmentation
GO:0006401 RNA catabolic process
GO:0006915 apoptotic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dk5, PDBe:5dk5, PDBj:5dk5
PDBsum5dk5
PubMed27529560
UniProtQ10905|CRN4_CAEEL 3'-5' exonuclease crn-4 (Gene Name=crn-4)

[Back to BioLiP]