Structure of PDB 5lu4 Chain A Binding Site BS01

Receptor Information
>5lu4 Chain A (length=850) Species: 4227 (Flaveria trinervia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKRVFTFGKGRSEGNRDMKSLLGGKGANLAEMSSIGLSVPPGLTISTEAC
EEYQQNGKSLPPGLWDEISEGLDYVQKEMSASLGDPSKPLLLSVRSGAAI
SMPGMMDTVLNLGLNDEVVAGLAGKSGARFAYDSYRRFLDMFGNVVMGIP
HSLFDEKLEQMKAEKGIHLDTDLTAADLKDLVEKYKNVYVEAKGEKFPTD
PKKQLELAVNAVFDSWDSPRANKYRSINQITGLKGTAVNIQSMVFGNMGN
TSGTGVLFTRNPSTGEKKLYGEFLINAQGEDVVAGIRTPEDLGTMETCMP
EAYKELVENCEILERHYKDMMDIEFTVQENRLWMLQCRTGKRTGKGAVRI
AVDMVNEGLIDTRTAIKRVETQHLDQLLHPQFEDPSAYKSHVVATGLPAS
PGAAVGQVCFSAEDAETWHAQGKSAILVRTETSPEDVGGMHAAAGILTAR
GGMTSHAAVVARGWGKCCVSGCADIRVNDDMKIFTIGDRVIKEGDWLSLN
GTTGEVILGKQLLAPPAMSNDLEIFMSWADQARRLKVMANADTPNDALTA
RNNGAQGIGLCRTEHMFFASDERIKAVRKMIMAVTPEQRKVALDLLLPYQ
RSDFEGIFRAMDGLPVTIRLLDPPLHEFLIYSKIENLSEVNPMLGFRGCR
LGISYPELTEMQVRAIFQAAVSMTNQGVTVIPEIMVPLVGTPQELRHQIS
VIRGVAANVFAEMGVTLEYKVGTMIEIPRAALIAEEIGKEADFFSFGTND
LTQMTFGYSRDDVGKFLQIYLAQGILQHDPFEVIDQKGVGQLIKMATEKG
RAANPSLKVGICGEHGGEPSSVAFFDGVGLDYVSCSPFRVPIARLAAAQV
Ligand information
Ligand IDADP
InChIInChI=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
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5lu4 Chain A Residue 901 [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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PDB5lu4 Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		K25 S93 R95 T108 L110 S242 M243 V244 G279 E280 E324 L335 Q336
Binding residue
(residue number reindexed from 1)		K25 S93 R95 T108 L110 S242 M243 V244 G279 E280 E324 L335 Q336
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K25 R95 G104 M106 R338 H456 E748 S767 D772 C834 Y854
Catalytic site (residue number reindexed from 1) K25 R95 G104 M106 R338 H456 E726 S745 D750 C812 Y832
Enzyme Commision number 2.7.9.1: pyruvate, phosphate dikinase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0046872 metal ion binding
GO:0050242 pyruvate, phosphate dikinase activity
Biological Process
GO:0006090 pyruvate metabolic process
GO:0015979 photosynthesis
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0009507 chloroplast

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5lu4, PDBe:5lu4, PDBj:5lu4
PDBsum5lu4
PubMed28470715
UniProtP22221|PPDK_FLATR Pyruvate, phosphate dikinase, chloroplastic (Gene Name=PPDK)

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