Structure of PDB 3cmu Chain A Binding Site BS13

Receptor Information
>3cmu Chain A (length=1937) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE
GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSG
AVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSN
TLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGEN
VVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEK
AGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLAIDENKQK
ALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPM
GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLG
VDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGE
IGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFGNPET
TTGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPFKQA
EFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAW
LKDNPETAKEIEKKVRELLLSNPNSAIDENKQKALAAALGQIEKQFGKGS
IMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTL
TLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQA
LEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAM
RKLAGNLKQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDI
RRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELV
DLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRE
LLLSNPNSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETIST
GSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAF
IDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIV
VDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFI
NQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSET
RVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYS
YKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNSAIDENKQKA
LAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMG
RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGV
DIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEI
GDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFGNPETT
TGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAE
FQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWL
KDNPETAKEIEKKVRELLLSNPNSAIDENKQKALAAALGQIEKQFGKGSI
MRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLT
LQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQAL
EICDALARSGAVDVIVVDSVAALTPKAEIEMGLAARMMSQAMRKLAGNLK
QSNTLLIFINQIRNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSE
TRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWY
SYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL
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 chain3cmu Chain A Residue 3502 [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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PDB3cmu Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
Resolution4.2 Å
Binding residue
(original residue number in PDB)		S3069 S3070 G3071 K3072 T3073 T3074 Y3103 Y3264 N4249 K4250 I4251 A4252 A4253 P4254
Binding residue
(residue number reindexed from 1)		S1027 S1028 G1029 K1030 T1031 T1032 Y1061 Y1222 N1540 K1541 I1542 A1543 A1544 P1545
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:0008094 ATP-dependent activity, acting on DNA
GO:0016887 ATP hydrolysis activity
GO:0140297 DNA-binding transcription factor binding
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0000725 recombinational repair
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006974 DNA damage response
GO:0009432 SOS response
GO:0010212 response to ionizing radiation
GO:0019985 translesion synthesis
GO:0035825 homologous recombination
GO:0048870 cell motility
Cellular Component
GO:0005737 cytoplasm
GO:0009355 DNA polymerase V complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3cmu, PDBe:3cmu, PDBj:3cmu
PDBsum3cmu
PubMed18497818
UniProtP0A7G6|RECA_ECOLI Protein RecA (Gene Name=recA)

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