Structure of PDB 8ojd Chain A Binding Site BS03

Receptor Information
>8ojd Chain A (length=976) Species: 10306 (Human alphaherpesvirus 1 strain KOS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCGGD
ERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEHAY
GMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAVHVYGTRQYFYMNKE
EVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDVYY
YETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDATTRFILDNPGF
VTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGMSDLP
AYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEHVL
LFSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYGPE
FVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSHFQ
KRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYRDI
PAYYAAGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGINIT
RTIYDGQQIRVFTCLLRLADQKGFILPDTQGRVLDPTSGFHVNPVVVFDF
ASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAH
VRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVY
GFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPE
AADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAVGDKMASHISRALF
LPPIKLECEKTFTKLLLIAKKKYIGVIYGGKMLIKGVDLVRKNNCAFINR
TSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAH
RRITDPERDIQDFVLTAELSRHPRAYTNKRLAHLTVYYKLMARRAQVPSI
KDRIPYVIVAQTREVEETVARLAALR
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain8ojd Chain A Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ojd Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM
Resolution2.46 Å
Binding residue
(original residue number in PDB)		D368 Y465 D471
Binding residue
(residue number reindexed from 1)		D308 Y405 D411
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.26.4: ribonuclease H.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0004519 endonuclease activity
GO:0004523 RNA-DNA hybrid ribonuclease activity
GO:0005515 protein binding
GO:0008409 5'-3' exonuclease activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0039686 bidirectional double-stranded viral DNA replication
GO:0039693 viral DNA genome replication
Cellular Component
GO:0042025 host cell nucleus
GO:0042575 DNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ojd, PDBe:8ojd, PDBj:8ojd
PDBsum8ojd
PubMed38806233
UniProtP04293|DPOL_HHV11 DNA polymerase catalytic subunit (Gene Name=UL30)

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