Structure of PDB 8ojd Chain A

Receptor sequence

>8ojdA (length=976) Species: 10306 (Human alphaherpesvirus 1 strain KOS)

PTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCGGD
ERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEHAY
GMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAVHVYGTRQYFYMNKE
EVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDVYY
YETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDATTRFILDNPGF
VTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGMSDLP
AYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEHVL
LFSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYGPE
FVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSHFQ
KRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYRDI
PAYYAAGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGINIT
RTIYDGQQIRVFTCLLRLADQKGFILPDTQGRVLDPTSGFHVNPVVVFDF
ASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAH
VRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVY
GFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPE
AADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAVGDKMASHISRALF
LPPIKLECEKTFTKLLLIAKKKYIGVIYGGKMLIKGVDLVRKNNCAFINR
TSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAH
RRITDPERDIQDFVLTAELSRHPRAYTNKRLAHLTVYYKLMARRAQVPSI
KDRIPYVIVAQTREVEETVARLAALR

3D structure

• PDB: 8ojd Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM
• Chain: A
• Resolution: 2.46 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.26.4: ribonuclease H.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	E370 C371 F381 Y465 N466 F470 F509 Y526 Y538 Y557 K960 A1035 E1036 R1039 T1045 L1049 H1051 R1071	E310 C311 F321 Y405 N406 F410 F449 Y466 Y478 Y497 K842 A917 E918 R921 T927 L931 H933 R953
BS02	dna	A	Q506 F509 R959 N1046 R1048	Q446 F449 R841 N928 R930
BS03	CA	A	D368 Y465 D471	D308 Y405 D411

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

External links

• PDB: RCSB:8ojd, PDBe:8ojd, PDBj:8ojd
• PDBsum: 8ojd
• PubMed: 38806233
• UniProt: P04293|DPOL_HHV11 DNA polymerase catalytic subunit (Gene Name=UL30)