Structure of PDB 3cmv Chain H Binding Site BS06

Receptor Information
>3cmv Chain H (length=1173) 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
AVDVIVVDSVAALTPKAEIEGEISHMGLAARMMSQAMRKLAGNLKQSNTL
LIFINQGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAP
FKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN
ATAWLKDNPETAKEIEKKVRELLLKQKALAAALGQIEKQFGKGSIMRLGE
DRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIA
AAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDA
LARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGN
LKQSNTLLIFINQGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVV
KNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEK
IGQGKANATAWLKDNPETAKEIEKKVRELLLKQKALAAALGQIEKQFGKG
SIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTT
LTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQ
ALEICDALARSGAVDVIVVDSVAALTPKAEIEGLAARMMSQAMRKLAGNL
KQSNTLLIFINQGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVK
NKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKI
GQGKANATAWLKDNPETAKEIEKKVRELLLKQKALAAALGQIEKQFGKGS
IMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTL
TLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQA
LEICDALARSGAVDVIVVDSVAALTPLAARMMSQAMRKLAGNLKQSNTLL
IFINQGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPF
KQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANA
TAWLKDNPETAKEIEKKVRELLL
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain3cmv Chain H Residue 2400 [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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PDB3cmv Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		E2068 S2069 G2071 K2072 T2073 T2074
Binding residue
(residue number reindexed from 1)		E644 S645 G647 K648 T649 T650
Annotation score3
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3cmv, PDBe:3cmv, PDBj:3cmv
PDBsum3cmv
PubMed18497818
UniProtP0A7G6|RECA_ECOLI Protein RecA (Gene Name=recA)

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