Structure of PDB 5vu7 Chain A Binding Site BS03

Receptor Information
>5vu7 Chain A (length=756) Species: 311400 (Thermococcus kodakarensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYFYALLKDDSAIEE
VKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDVPAIRDKI
REHPAVIDIYEYDIPFAKRYLIDKGLVPMEGDEELKMLAFAIATLYHEGE
EFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKE
KDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMGDRFAV
EVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWE
TGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTG
NLVEWFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWENI
VYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFPGFIP
SLLGDLLEERQKIKKKMKATIDPIERKLLDYRQRRIKILANSYYGYYGYA
RARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIPG
ADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEE
GKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKL
SKYEVPPEKLVIHIQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVIS
YIVLKGSGRIGDRAIPFDEFDPTKHKYDAEYYIENQVLPAVERILRAFGY
RKEDLR
Ligand information
Ligand IDFA2
InChIInChI=1S/C9H12N5O6P/c10-7-5-8(12-2-11-7)14(3-13-5)9-6(15)4(1-19-9)20-21(16,17)18/h2-4,6,9,15H,1H2,(H2,10,11,12)(H2,16,17,18)/t4-,6+,9+/m0/s1
InChIKeyIJEJRDCFMFEDGL-AFEQZKEHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](CO3)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3OC[CH](O[P](O)(O)=O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3OC[C@H](O[P](O)(O)=O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(CO3)OP(=O)(O)O)O)N
ACDLabs 10.04O=P(O)(O)OC3COC(n2cnc1c(ncnc12)N)C3O
FormulaC9 H12 N5 O6 P
Name5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL DIHYDROGEN PHOSPHATE
ChEMBL
DrugBankDB02454
ZINCZINC000058638540
PDB chain5vu7 Chain A Residue 803 [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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PDB5vu7 Structural basis for TNA synthesis by an engineered TNA polymerase.
Resolution2.72 Å
Binding residue
(original residue number in PDB)		L408 Y409 Y494 D542
Binding residue
(residue number reindexed from 1)		L408 Y409 Y494 D542
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
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:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0071897 DNA biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5vu7, PDBe:5vu7, PDBj:5vu7
PDBsum5vu7
PubMed29180809
UniProtD0VWU9

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