Structure of PDB 8oma Chain A Binding Site BS03

Receptor Information
>8oma Chain A (length=760) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIGVVGVKMSQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQKECV
LPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQDLNRLLKGKKG
EQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFSQYM
KLDIAAVRALNLFQGDTTGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDK
NRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQRQAANLQD
CYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEM
IETTLDMDQVENHEFLVKPSFDPNLSELREIMNDLEKKMQSTLISAARDL
GLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTN
SKLTSLNEEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLD
AVVSFAHVSNGAPVPYVRPAILEKGQGRIILKASRHACVEVQDEIAFIPN
DVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVS
IVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDELGRG
TSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNNLHVT
ALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEE
FQYEQGEKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIAKNNSFVN
EIISRIKVTT
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8oma Chain A Residue 2000 [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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PDB8oma MutSbeta bound to 61bp homoduplex DNA
Resolution3.29 Å
Binding residue
(original residue number in PDB)		I648 F650 N671 M672 G673 G674 K675 S676 T677 H783 Y815
Binding residue
(residue number reindexed from 1)		I495 F497 N518 M519 G520 G521 K522 S523 T524 H630 Y662
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0000400 four-way junction DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003684 damaged DNA binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016887 ATP hydrolysis activity
GO:0019237 centromeric DNA 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:0032143 single thymine insertion binding
GO:0032181 dinucleotide repeat insertion binding
GO:0032357 oxidized purine DNA binding
GO:0032405 MutLalpha complex binding
GO:0042803 protein homodimerization activity
GO:0043531 ADP binding
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0001701 in utero embryonic development
GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
GO:0006119 oxidative phosphorylation
GO:0006281 DNA repair
GO:0006298 mismatch repair
GO:0006301 postreplication repair
GO:0006302 double-strand break repair
GO:0006312 mitotic recombination
GO:0006974 DNA damage response
GO:0007281 germ cell development
GO:0008340 determination of adult lifespan
GO:0008584 male gonad development
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010165 response to X-ray
GO:0010224 response to UV-B
GO:0016446 somatic hypermutation of immunoglobulin genes
GO:0016447 somatic recombination of immunoglobulin gene segments
GO:0019724 B cell mediated immunity
GO:0030183 B cell differentiation
GO:0031573 mitotic intra-S DNA damage checkpoint signaling
GO:0042771 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0043524 negative regulation of neuron apoptotic process
GO:0043570 maintenance of DNA repeat elements
GO:0045190 isotype switching
GO:0045910 negative regulation of DNA recombination
GO:0048298 positive regulation of isotype switching to IgA isotypes
GO:0048304 positive regulation of isotype switching to IgG isotypes
GO:0051096 positive regulation of helicase activity
GO:0051726 regulation of cell cycle
GO:0071168 protein localization to chromatin
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0016020 membrane
GO:0032301 MutSalpha complex
GO:0032302 MutSbeta complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8oma, PDBe:8oma, PDBj:8oma
PDBsum8oma
PubMed
UniProtP43246|MSH2_HUMAN DNA mismatch repair protein Msh2 (Gene Name=MSH2)

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