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Structure of PDB 6m5v Chain A Binding Site BS01

Receptor Information
>6m5v Chain A (length=585) Species: 10299 (Human alphaherpesvirus 1 strain 17) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDALRVPFLDFATATPKRHQTVVPGVGTLHDCCEHSPLFSAVARRLLFNS
LVPAQLKGRDFGGDHTAKLEFLAPELVRAVARLRFKECAPADVVPQRNAY
YSVLNTFQALHRSEAFRQLVHFVRDFAQLLKTSFRASSLTYGTLELFQKM
ILMHATYFLAAVLLGDHAEQVNTFLRLVFEIPLFSDAAVRHFRQRATVFL
VPRRHGKTWFLVPLIALSLASFRGIKIGYTAHIRTEPVFEEIDACLRGWF
GSARVDHVKGETISFSFPDGSRSTIVFASSHQDFNLLFVDEANFIRPDAV
QTIMGFLNQANCKIIFVSSTNTGKASTSFLYNLRGAADELLNVVTYICDD
HMPRVVTHTNATACSCPVLTKSAGERFLLYRPSTTTNSGLMAPDLYVYVD
PAFTANTRASGTGVAVVGRYRDDYIIFALEHFFLRALTGSAPADIARCVV
HSLTQVLALHPGAFRGVRVAVEGNSSQDSAVAIATHVHTEMHRGPELLFY
HCEPPGSAVLYPFFLLNKQKTPAFEHFIKKFNSGGVMASQEIVSATVRLQ
TDPVEYLLEQLNNLTSDDLMVAVIMAIYLAGPPHT
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6m5v Chain A Residue 801 [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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PDB6m5v Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation.
Resolution4.5 Å
Binding residue
(original residue number in PDB)		T200 E202 G263 K264 T265 W266 C430
Binding residue
(residue number reindexed from 1)		T143 E145 G206 K207 T208 W209 C364
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.-.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
Biological Process
GO:0051276 chromosome organization
Cellular Component
GO:0042025 host cell nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6m5v, PDBe:6m5v, PDBj:6m5v
PDBsum6m5v
PubMed32328903
UniProtP04295|TRM3_HHV11 Tripartite terminase subunit 3 (Gene Name=TRM3)

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