Structure of PDB 6p0b Chain A Binding Site BS04

Receptor Information
>6p0b Chain A (length=642) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMV
ETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVA
QATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFR
DIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSV
LAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCE
VPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFE
EAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIK
LPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYA
FDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAE
FLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDL
VVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHH
QSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAAR
GLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQS
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain6p0b Chain C Residue 101 [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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PDB6p0b Two-tiered enforcement of high-fidelity DNA ligation.
Resolution2.203 Å
Binding residue
(original residue number in PDB)		E566 Y567 K568 Y569 R573 E621 F660 M723 K725 K744
Binding residue
(residue number reindexed from 1)		E307 Y308 K309 Y310 R314 E362 F401 M464 K466 K485
Annotation score4
Enzymatic activity
Enzyme Commision number 6.5.1.1: DNA ligase (ATP).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003909 DNA ligase activity
GO:0003910 DNA ligase (ATP) activity
GO:0005524 ATP binding
Biological Process
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0071897 DNA biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6p0b, PDBe:6p0b, PDBj:6p0b
PDBsum6p0b
PubMed31780661
UniProtP18858|DNLI1_HUMAN DNA ligase 1 (Gene Name=LIG1)

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