Structure of PDB 7tve Chain D Binding Site BS02

Receptor Information
>7tve Chain D (length=445) Species: 580240 (Saccharomyces cerevisiae W303) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILTAITI
GLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEII
VERIIKRDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQ
DAARSFLTASTSQDKYSHFMKGTLLQEITENLLYASAIHDSAQENMALHL
ENLKSLKAEYEDAKKLLRELNQTSDLNERKMLLQAKSLDTQEEIKRELDK
VSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNS
LKARDQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYIL
TTNDEKARNVDTLSGGEKSFSQMALLLATWKPMRSRIIALDQFDVFMDQV
NRKIGTTLIVKKLKDIARTQTIIITPQDIGKIADIDSSGVSIHRM
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 chain7tve Chain E Residue 1101 [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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PDB7tve Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		R1014 S1020 G1021 E1023
Binding residue
(residue number reindexed from 1)		R358 S364 G365 E367
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003697 single-stranded DNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0019789 SUMO transferase activity
Biological Process
GO:0000724 double-strand break repair via homologous recombination
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006310 DNA recombination
GO:0016925 protein sumoylation
GO:0032204 regulation of telomere maintenance
GO:0051304 chromosome separation
GO:0071139 resolution of DNA recombination intermediates
GO:0140588 chromatin looping
GO:1990683 DNA double-strand break attachment to nuclear envelope
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005739 mitochondrion
GO:0030915 Smc5-Smc6 complex
GO:0035861 site of double-strand break

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7tve, PDBe:7tve, PDBj:7tve
PDBsum7tve
PubMed35648833
UniProtQ12749|SMC6_YEAST Structural maintenance of chromosomes protein 6 (Gene Name=SMC6)

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