Structure of PDB 7luf Chain B

Receptor sequence

>7lufB (length=1054) Species: 10298 (Human alphaherpesvirus 1)

NFYNPYLAPVGPTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHL
KRAPKVYCGGDERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHV
YDILENVEHAYGMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAVHVY
GTRQYFYMNKEEVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFE
AEVVERTDVYYYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDA
TTRFILDNPGFVTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADN
LAIEGGMSDLPAYKLMCFDIACKAGGEDELAFPVAGHPEDLVIQISCLLY
DLSTTALEHVLLFSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLA
FMTLVKQYGPEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVF
RVWDIGQSHFQKRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLK
DKKKDLSYRDIPAYYAAGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELS
AVARLAGINITRTIYDGQQIRVFTCLLRLADQKGFILPDTQRHVGYQGAR
VHDPTSGFHVNPVVGFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGK
DYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEA
VLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATRE
YVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAA
GLTAMGDKMASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGVIYGGKM
LIKGVDLVRKNNCAFINRTSRALVDLLFYDDTVSGAAAALAERPAEEWLA
RPLPEGLQAFGAVLVDAHRRITDPERDIQDFVLTAELSRHPRAYTNKRLA
HLTVYYKLMARRAQVPSIKDRIPYVIVAQTREVEETVARLAALREVSELA
EDPAYAIAHGVALNTDYYFSHLLGAACVTFKALFGNNAKITESLLKRFIP
EVWH

3D structure

• PDB: 7luf Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase.
• Chain: B
• Resolution: 3.5 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	B	F509 Q510 K514 G616 Q617 Q618 Q640 G695 Y696 Q697 G698 V701 L827 K938 K939 K940 R959 R1048 V1139 S1140 Y1160 H1164	F460 Q461 K465 G567 Q568 Q569 Q591 G595 Y596 Q597 G598 V601 L727 K838 K839 K840 R859 R948 V996 S997 Y1017 H1021
BS02	dna	B	K534 D888 K939 Y941 K953 G954 R959 E1036 R1039 Y1044 T1045 N1046 R1071	K485 D788 K839 Y841 K853 G854 R859 E936 R939 Y944 T945 N946 R971
BS03	YE4	B	Q617 Q618 L721 Y722 S816 G819 F820 V823	Q568 Q569 L621 Y622 S716 G719 F720 V723	BindingDB: IC50=600nM

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:7luf, PDBe:7luf, PDBj:7luf
• PDBsum: 7luf
• PubMed: 34031403
• UniProt: P04293|DPOL_HHV11 DNA polymerase catalytic subunit (Gene Name=UL30)