Structure of PDB 6ppj Chain A Binding Site BS02

Receptor Information
>6ppj Chain A (length=901) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STLLEPGSNGVVRLLGGPGTGKSSLLVDTAVQHILDPESVLLLTGSARLR
TAARAAITARLGVVREPLVRTVHSYAFAVLRLAAQPPPRLITSAEQDGII
RELLAGDLEDGPVGWPEQLWPALTTAGFATELRDLMARCTERGVDPIALQ
RLGRTAKRPEWLAAGRFAQAYEQIMLLPALGAAELVGAALEALGADDELL
DTERNRIKLLLVDDAQHLDPQAARLVRALAAGTGLTVIAGDPDQSVVLLR
DDTHPAITLTQSYRCAPEIASAITGLGQRLPTRHWTGNPQREGTVTVRLA
ASTHAEGTMIADALRRAHLVDGIPWSQMAVIVRSVPALARALTAAGVPVQ
DVPVGRQPAAAALLTVLDVTATGHLDADSAVALLTGPIGRVDPVTLRQLR
RALRRAPPRDFGDLLVDAIEREPKGLSAEHARTLRRLRAVLTAARRSPRY
TLWQAWHASGLQRRWLAASVGAQADRDLDAVTTLFDVADQYVNRLRGLVD
HVTRLAEAVAVLSVHGALAGEWDFVVIAGVQEGLWPNMIPRGGVLGTQHL
VDVLDGVADMTDRTVSTRAPLVAEERRLLMAAMGRARTRVMITAVDSLLP
SPFCAEISAWATPPLVAPRVLAPSALVGRLRAVVCAPAVDDDARACAAAQ
LARLAAAGVPGADPSQWHAMTSLTTEEPLWSEHVVTLSPSTLQMLTDCPL
RWLLERHGGDDGDVRSTVGSLVHALVSETESQLVNELEKVWDDLPYDAKW
YSDNELARHRAMLETFTRWREDTRRQLTEVATEIPVEGIVVEPPGVRVRG
RLDRLERDLVVVALKTGKSPVTKDDAQNHAQLAMYQLAVAAGLGGKLVYL
GKATEREQDPKRAEWLETVGEAAAATAGPRFVARVNNGCANCPVRSSCPA
Q
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 chain6ppj Chain A Residue 1102 [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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PDB6ppj Structures and single-molecule analysis of bacterial motor nuclease AdnAB illuminate the mechanism of DNA double-strand break resection.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		G32 T33 G34 K35 S36 S37 Y313 R679
Binding residue
(residue number reindexed from 1)		G19 T20 G21 K22 S23 S24 Y263 R585
Annotation score3
Enzymatic activity
Enzyme Commision number 5.6.2.4: DNA 3'-5' helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0004527 exonuclease activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016853 isomerase activity
GO:0043138 3'-5' DNA helicase activity
Biological Process
GO:0000725 recombinational repair
GO:0006281 DNA repair
GO:0032508 DNA duplex unwinding
Cellular Component
GO:0005829 cytosol
GO:0033202 DNA helicase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ppj, PDBe:6ppj, PDBj:6ppj
PDBsum6ppj
PubMed31740608
UniProtA0QTR9

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