Structure of PDB 7kr4 Chain A Binding Site BS04

Receptor Information
>7kr4 Chain A (length=639) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNDMDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLR
MVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKA
VAQATGRQLESVRAEAAEKGDVGLVAENSRSTPPPPLTASGVFSKFRDIA
RLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAA
LSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPD
LDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAA
FTCEYKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPS
VTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDL
IYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLE
QSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVI
GAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSL
KALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLV
DSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQS
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 chain7kr4 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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PDB7kr4 High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		K568 Y569 R573 E621 F660 M723 K725 K744
Binding residue
(residue number reindexed from 1)		K306 Y307 R311 E359 F398 M461 K463 K482
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:7kr4, PDBe:7kr4, PDBj:7kr4
PDBsum7kr4
PubMed33473124
UniProtP18858|DNLI1_HUMAN DNA ligase 1 (Gene Name=LIG1)

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