Structure of PDB 5nwl Chain N Binding Site BS01

Receptor Information
>5nwl Chain N (length=301) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAK
ADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETG
SITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPER
LLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLI
VDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVV
GNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDAK
D
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 chain5nwl Chain N Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5nwl Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA.
Resolution3.93 Å
Binding residue
(original residue number in PDB)		R130 G132 K133 T134 Q135 R170 Q268 R310 I329 N330
Binding residue
(residue number reindexed from 1)		R110 G112 K113 T114 Q115 R150 Q248 R272 I291 N292
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000150 DNA strand exchange activity
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003682 chromatin 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:0017116 single-stranded DNA helicase activity
GO:0019899 enzyme binding
GO:0042802 identical protein binding
GO:0070182 DNA polymerase binding
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0000722 telomere maintenance via recombination
GO:0000724 double-strand break repair via homologous recombination
GO:0000730 DNA recombinase assembly
GO:0006259 DNA metabolic process
GO:0006268 DNA unwinding involved in DNA replication
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006312 mitotic recombination
GO:0006974 DNA damage response
GO:0007131 reciprocal meiotic recombination
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0010833 telomere maintenance via telomere lengthening
GO:0031297 replication fork processing
GO:0032200 telomere organization
GO:0036297 interstrand cross-link repair
GO:0042148 DNA strand invasion
GO:0051106 positive regulation of DNA ligation
GO:0051321 meiotic cell cycle
GO:0070192 chromosome organization involved in meiotic cell cycle
GO:0071312 cellular response to alkaloid
GO:0071479 cellular response to ionizing radiation
GO:0072711 cellular response to hydroxyurea
GO:0072757 cellular response to camptothecin
GO:1990414 replication-born double-strand break repair via sister chromatid exchange
GO:1990426 mitotic recombination-dependent replication fork processing
GO:1990918 double-strand break repair involved in meiotic recombination
GO:2000001 regulation of DNA damage checkpoint
Cellular Component
GO:0000152 nuclear ubiquitin ligase complex
GO:0000228 nuclear chromosome
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0000793 condensed chromosome
GO:0000794 condensed nuclear chromosome
GO:0000800 lateral element
GO:0001673 male germ cell nucleus
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016605 PML body
GO:0032991 protein-containing complex
GO:0035861 site of double-strand break
GO:0048471 perinuclear region of cytoplasm
GO:0099182 presynaptic intermediate filament cytoskeleton

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nwl, PDBe:5nwl, PDBj:5nwl
PDBsum5nwl
PubMed29507080
UniProtQ06609|RAD51_HUMAN DNA repair protein RAD51 homolog 1 (Gene Name=RAD51)

[Back to BioLiP]