Structure of PDB 3cmx Chain D Binding Site BS16

Receptor Information

>3cmx Chain D (length=1603) Species: 83333 (Escherichia coli K-12)

VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE
GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSG
AVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSN
TLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGEN
VVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEK
AGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNSAID
ENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGA
GGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIY
ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKA
EIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMF
GNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAA
PFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKA
NATAWLKDNPETAKEIEKKVRELLLSNPNSAIDENKQKALAAALGQIEKQ
FGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESS
GKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPD
TGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARM
MSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYAS
VRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINF
YGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLKDNPETAKEIE
KKVRELLLSNPNSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDV
ETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREG
KTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA
VDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNT
LLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENV
VGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKA
GAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNSAIDE
NKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAG
GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYA
RKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAE
ARMMSQAMRKLAGNLKQSNTLLIFINQIRNPETTTGGNALKFYASVRLDI
RRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELV
DLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRE
LLL

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 3cmx Chain D Residue 3502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3cmx Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): S3069 G3071 K3072 T3073 T3074 Y3103 Y3264 N4249 K4250 I4251 A4252 A4253 P4254
• Binding residue (residue number reindexed from 1): S1032 G1034 K1035 T1036 T1037 Y1066 Y1227 N1524 K1525 I1526 A1527 A1528 P1529
• Annotation score: 5

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

External links

• PDB: RCSB:3cmx, PDBe:3cmx, PDBj:3cmx
• PDBsum: 3cmx
• PubMed: 18497818
• UniProt: P0A7G6|RECA_ECOLI Protein RecA (Gene Name=recA)