Structure of PDB 8b1t Chain B Binding Site BS02

Receptor Information
>8b1t Chain B (length=1141) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPL
TVEELLVVTFTEAATAELRGRIRSNIHELRIACLRETTDNPLYERLLEEI
DDKAQAAQWLLLAERQMDEAAVFTIHGFCQRMLNLNAFESGMLFEQQLIE
DESLLRYQACADFWRRHCYPLPREIAQVVFETWKGPQALLRDINRYLQGE
APVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELDALIESSGIDR
RKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFSQRFLEDRTKAGGET
PRHPLFEAIDQLLAEPLSIRDLVITRALAEIRETVAREKRRRGELGFDDM
LSRLDSALRSESGEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHHQ
PETALLLIGDPKQAIYAFRGADIFTYMKARSEVHAHYTLDTNWRSAPGMV
NSVNKLFSQTDDAFMFREIPFIPVKSAGKNQALRFVFKGETQPAMKMWLM
EGESCGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPVRASDI
SVLVRSRQEAAQVRDALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVM
TPERENTLRSALATSMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRK
RGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGTQLESE
HALVRWLSQHILEPDSNASSQQMRLESDKHLVQIVTIHKSKGLEYPLVWL
PFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAEAERLAEDLRLLYV
ALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLR
TCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNWRVT
SYSGLQQTPHQFPRGASPGTFLHSLFEDLDFTQPVDPNWVREKLELGGFE
SQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEFYLPISEPLIA
SQLDTLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLAYKS
NWLGEDSSAYTQQAMAAAMQAHRYDLQYQLYTLALHRYLRHRIADYDYEH
HFGGVIYLFLRGVDKEHPQQGIYTTRPNAGLIALMDEMFAG
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 chain8b1t Chain B Residue 1501 [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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PDB8b1t Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		G26 G28 K29 T30 F31 W447 R448 R808
Binding residue
(residue number reindexed from 1)		G22 G24 K25 T26 F27 W443 R444 R804
Annotation score3
Enzymatic activity
Enzyme Commision number 3.1.11.5: exodeoxyribonuclease V.
5.6.2.4: DNA 3'-5' helicase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0004520 DNA endonuclease activity
GO:0004527 exonuclease activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0008854 exodeoxyribonuclease V activity
GO:0015616 DNA translocase activity
GO:0016787 hydrolase activity
GO:0016853 isomerase activity
GO:0016887 ATP hydrolysis activity
GO:0043138 3'-5' DNA helicase activity
GO:0046872 metal ion binding
Biological Process
GO:0000724 double-strand break repair via homologous recombination
GO:0000725 recombinational repair
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0009314 response to radiation
GO:0032508 DNA duplex unwinding
GO:0044355 clearance of foreign intracellular DNA
Cellular Component
GO:0005829 cytosol
GO:0009338 exodeoxyribonuclease V complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8b1t, PDBe:8b1t, PDBj:8b1t
PDBsum8b1t
PubMed36533901
UniProtP08394|RECB_ECOLI RecBCD enzyme subunit RecB (Gene Name=recB)

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