Structure of PDB 5yk4 Chain B Binding Site BS01

Receptor Information
>5yk4 Chain B (length=767) Species: 242231 (Neisseria gonorrhoeae FA 1090) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAVSPMMQQYLGIKAQHTDKLVFYRMGDFYELFLDDAVEAAKLLDITLTT
RGQMDGVPIKMAGVPFHAAEQYLARLVKLGKSVAICEQVGEVGAGKGPVE
RKVVRIVTPGTLTDSALLEDKETNRIVAVSPDKKYIGLAWASLQSGEFKT
KLTTADKLNDELARLQAAEILLPDSKNAPQLQTASGVTRLNAWQFAADAG
EKLLTEYFGCQDLRGFGLDSKEHAVSIGAAGALLNYIRLTQNLMPQHLDG
LSLETDSQYIGMDAATRRNLEITQTLSGKKTPTLFSILDGCATHMGSRLL
ALWLHHPLRNRAHIRARQEAVTALESQYEPLQCHLKSIADIERIAARIAV
GNARPRDLASLRDSLFELAQIDLSATGSSLLETLKAVFPETLPVAETLKA
AVMPEPSVWLKDGNVINHGFHPELDELRRIQNHGDEFLLDLEAKERERTG
LSTLKVEFNRVHGFYIELSKTQAEQAPADYQRRQTLKNAERFITPELKAF
EDKVLTAQDQALALEKQLFDGVLKNLRTALPQLQKAAKAAAALDVLSTFS
ALAKERNFVRPEFADYPVVHIENGRHPVVEQQVRHFTANHTDLDHKHRLM
LLTGPNMGGKSTYMRQVALIVLLAHTGCFVPADAATIGPVDQIFTRVEMS
ETAYILHHATEQSIVLMDEVGRGTSTFDGLALAHAIAEHLLQKNKSFSLF
ATHYFELTYLPEAHAAAVNMHLSALEQGRDIVFLHQIQPGPAGKSYGIAV
AKLAGLPVRALKAAQKH
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 chain5yk4 Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yk4 Mechanism of formation of a toroid around DNA by the mismatch sensor protein.
Resolution2.97 Å
Binding residue
(original residue number in PDB)		F589 T590 N609 G612 K613 S614 T615 H753
Binding residue
(residue number reindexed from 1)		F586 T587 N606 G609 K610 S611 T612 H735
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0005524 ATP binding
GO:0030983 mismatched DNA binding
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0006281 DNA repair
GO:0006298 mismatch repair
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yk4, PDBe:5yk4, PDBj:5yk4
PDBsum5yk4
PubMed29182773
UniProtQ5F5J4|MUTS_NEIG1 DNA mismatch repair protein MutS (Gene Name=mutS)

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