Structure of PDB 1xdp Chain A Binding Site BS03

Receptor Information
>1xdp Chain A (length=687) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQEKLYIEKELSWLSFNERVLQEAADKSNPLIERMRFLGIYSNNLDEFYK
VRFAELKRRIIISEEQGSNSHSRHLLGKIQSRVLKADQEFDGLYNELLLE
MARNQIFLINERQLSVNQQNWLRHYFKQYLRQHITPILINPDTDLVQFLK
DDYTYLAVEIIRGDTIRYALLEIPSDKVPRFVNLPPEAPRRRKPMILLDN
ILRYCLDDIFKGFFDYDALNAYSMKMTRDAEYDLVHEMEASLMELMSSSL
KQRLTAEPVRFVYQRDMPNALVEVLREKLTISRYDSIVPGGRYHNFKDFI
NFPNVGKANLVNKPLPRLRHIWFDKAQFRNGFDAIRERDVLLYYPYHTFE
HVLELLRQASFDPSVLAIKINIYRVAKDSRIIDSMIHAAHNGKKVTVVVE
LQARFDEEANIHWAKRLTEAGVHVIFSAPGLKIHAKLFLISRKENGEVVR
YAHIGTGNFNEKTARLYTDYSLLTADARITNEVRRVFNFIENPYRPVTFD
YLMVSPQNSRRLLYEMVDREIANAQQGLPSGITLKLNNLVDKGLVDRLYA
ASSSGVPVNLLVRGMCSLIPNLEGISDNIRAISIVDRYLEHDRVYIFENG
GDKKVYLSSADWMTRNIDYRIEVATPLLDPRLKQRVLDIIDILFSDTVKA
RYIDKELSNRYVPRGNRRKVRAQLAIYDYIKSLEQPE
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain1xdp Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1xdp Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis
Resolution2.5 Å
Binding residue
(original residue number in PDB)		F17 I41 N45 Y374 R375 R405 H435 Y468 R564 L590 H592
Binding residue
(residue number reindexed from 1)		F16 I40 N44 Y373 R374 R404 H434 Y467 R563 L589 H591
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.4.1: ATP-polyphosphate phosphotransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008976 polyphosphate kinase activity
GO:0016301 kinase activity
GO:0016776 phosphotransferase activity, phosphate group as acceptor
GO:0016778 diphosphotransferase activity
GO:0042803 protein homodimerization activity
GO:0043751 polyphosphate:AMP phosphotransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006793 phosphorus metabolic process
GO:0006799 polyphosphate biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009358 polyphosphate kinase complex
GO:0031241 periplasmic side of cell outer membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1xdp, PDBe:1xdp, PDBj:1xdp
PDBsum1xdp
PubMed15947782
UniProtP0A7B1|PPK1_ECOLI Polyphosphate kinase (Gene Name=ppk)

[Back to BioLiP]