Structure of PDB 8om9 Chain B Binding Site BS03

Receptor Information
>8om9 Chain B (length=816) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTPLELQYIEMKQQHKDAVLCVECGYKYRFFGEDAEIAARELNIYCHLDH
NFMTASIPTHRLFVHVRRLVAKGYKVGVVKQRKLTALYTKSTLIGEDVNP
LTSYLLCISENKENVRDKKKGNIFIGIVGVQPATGEVVFDSFQDSASRSE
LETRMSSLQPVELLLPSALSEQTEALIHRATSVRIRVERMDNIYFEYSHA
FQAVTEFYIVNLEKPVICSLAAIIKYLKEFNLEKMLSKPENFKQLSSKME
FMTINGTTLRNLEILQNQTDMKTKGSLLWVLDHTKTSFGRRKLKKWVTQP
LLKLREINARLDAVSEVLHSESSVFGQIENHLRKLPDIERGLCSIYHKKC
STQEFFLIVKTLYHLKSEFQAIIPAVNSHIQSDLLRTVILEIPELLSPVE
HYLKILNEQAAKVGDKTELFKDLSDFPLIKKRKDEIQGVIDEIRMHLQEI
RKILKNPSAQYVTVSGQEFMIEIKNSAVSCIPTDWVKVGSTKAVSRFHSP
FIVENYRHLNQLREQLVLDCSAEWLDFLEKFSEHYHSLCKAVHHLATVDC
IFSLAKVAKQGDYCRPTVQEERKIVIKNGRHPVIDVLLGEQDQYVPNNTD
LSEDSERVMIITGPNMGGKSSYIKQVALITIMAQIGSYVPAEEATIGIVD
GIFTRMSTFMEELTDTAEIIRKATSQSLVILDELGRGTSTHDGIAIAYAT
LEYFIRDVKSLTLFVTHYPPVCELEKNYSHQVGNYHMGFLVSEDFVTFLY
QITRGIAARSYGLNVAKLADVPGEILKKAAHKSKELEGLINTKRKRLKYF
AKLWTMHNAQDLQKWT
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 chain8om9 Chain B Residue 2000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8om9 MutSbeta bound to (CAG)2 DNA (open form)
Resolution3.32 Å
Binding residue
(original residue number in PDB)		Q876 Y877 V878 N898 K902 S903 S904 Y1057
Binding residue
(residue number reindexed from 1)		Q593 Y594 V595 N615 K619 S620 S621 Y750
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0019899 enzyme binding
GO:0030983 mismatched DNA binding
GO:0032137 guanine/thymine mispair binding
GO:0032139 dinucleotide insertion or deletion binding
GO:0032142 single guanine insertion binding
GO:0032181 dinucleotide repeat insertion binding
GO:0032357 oxidized purine DNA binding
GO:0042803 protein homodimerization activity
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0006281 DNA repair
GO:0006298 mismatch repair
GO:0006312 mitotic recombination
GO:0016447 somatic recombination of immunoglobulin gene segments
GO:0043570 maintenance of DNA repeat elements
GO:0045910 negative regulation of DNA recombination
GO:0051096 positive regulation of helicase activity
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016020 membrane
GO:0032302 MutSbeta complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8om9, PDBe:8om9, PDBj:8om9
PDBsum8om9
PubMed
UniProtP20585|MSH3_HUMAN DNA mismatch repair protein Msh3 (Gene Name=MSH3)

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