Structure of PDB 6wya Chain A Binding Site BS03

Receptor Information
>6wya Chain A (length=756) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYLYALLKDDSAIEE
VKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDVPAIMDKI
REHPAVIDIYEYDIPFAIRYLIDKGLVPMEGDEELKLLAFDIETLYHEGE
EFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKE
KDPDVLITYDGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMGDRFAV
EVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWE
TGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTG
NLVEWFLLRKAYERNELAPNKPDEKELARRHQSHEGGYIKEPERGLWENI
VYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFPGFIP
SLLGDLLEERQKIKKRMKATIDPIERKLLDYRQRAIKILANSLYGYYGYA
RARWYCKECAESVIAWGREYLTMTIKEIEEKYGFKVIYSDTDGFFATIPG
ADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGLFVTKKKYAVIDEE
GKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKL
SKYEVPPEKLVIHKQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVIS
YIVLKGSGRIVDRAIPFDEFDPTKHKYDAEYYIEKQVLPAVERILRAFGY
RKEDLR
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6wya Chain A Residue 804 [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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PDB6wya How a B family DNA polymerase has been evolved to copy RNA.
Resolution2.41 Å
Binding residue
(original residue number in PDB)		D141 E143 D315
Binding residue
(residue number reindexed from 1)		D141 E143 D315
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:6wya, PDBe:6wya, PDBj:6wya
PDBsum6wya
PubMed32817521
UniProtD0VWU9

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