Structure of PDB 8om5 Chain A Binding Site BS01

Receptor Information
>8om5 Chain A (length=828) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIK
YMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNNDWYLAYKAS
PGNLSQFESIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFS
NLEALLIQIGPKECVLPGETAGDMGKLRQIIQRGGILITERKKADFSTKD
IYQDLNRLLKGKKQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQ
FELTTFDFSQYMKLDIAAVRALNLFQSQSLAALLNKCKTPQGQRLVNQWI
KQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQR
QAANLQDCYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSD
FSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSELREIMNDLEKKMQSTL
ISAARDLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQK
NGVKFTNSKLTSLNEEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLN
DVLAQLDAVVSFAHVSNGAPVPYVRPAILEKGQGRIILKASRHACVEVQD
EIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVP
CESAEVSIVDCILARVGVSTFMAEMLETASILRSATKDSLIIIDELGRGT
STYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNNLHVTA
LTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEL
EREQGEKIIQEFLSKVLKQLKAEVIAKN
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 chain8om5 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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PDB8om5 DNA-free open form of MutSbeta
Resolution3.52 Å
Binding residue
(original residue number in PDB)		A649 F650 I651 N671 M672 G674 K675 S676 T677 Y815
Binding residue
(residue number reindexed from 1)		A603 F604 I605 N625 M626 G628 K629 S630 T631 Y761
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
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Biological Process
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Cellular Component
External links
PDB RCSB:8om5, PDBe:8om5, PDBj:8om5
PDBsum8om5
PubMed
UniProtP43246|MSH2_HUMAN DNA mismatch repair protein Msh2 (Gene Name=MSH2)

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