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BioLiP

Structure of PDB 5jvl Chain B Binding Site BS01

Receptor Information
>5jvl Chain B (length=520) Species: 4227 (Flaveria trinervia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FTRNPSTGEKKLYLVENCEILERHYKDMMDIRTGKRTGKGAVRIAVDMVN
EGLIDTRTAIKRVETQHLDQLLHPQFEDPSAYKSHVVATGLPASPGAAVG
QVCFSAEDAETWHAQGKSAILMTSHAAVVARGWGKCCVEGDWLSLNGTTG
EVILGKQLLAPPAMSNDLEIFMSWADQARRLKVMANADTPNDALTARNNG
AQGIGLCRTEHMFFASDERIKAVRKMIMAVTPEQRKVALDLLLPYQRSDF
EGIFRAMDGLPVTIRLLDPPLHEFLPEGDLEHIVNELAVDTGMSADEIYS
KIENLSEVNPMLGFRGCRLGISYPELTEMQVRAIFQAAVSMTNQGVTVIP
EIMVPLVGTPQELRHQISVIRGVAANVFAEMGVTLEYKVGTMIEIPRAAL
IAEEIGKEADFFSFGTNDLTQMTFGYSRDDVGKFLQIYLAQGILQHDPFE
VIDQKGVGQLIKMATEKGRAANPSLKVGICGEHGGEPSSVAFFDGVGLDY
VSCSPFRVPIARLAAAQVIV
Ligand information
Ligand IDPEP
InChIInChI=1S/C3H5O6P/c1-2(3(4)5)9-10(6,7)8/h1H2,(H,4,5)(H2,6,7,8)
InChIKeyDTBNBXWJWCWCIK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C=C(C(=O)O)OP(=O)(O)O
CACTVS 3.341OC(=O)C(=C)O[P](O)(O)=O
ACDLabs 10.04O=C(O)C(\OP(=O)(O)O)=C
FormulaC3 H5 O6 P
NamePHOSPHOENOLPYRUVATE
ChEMBLCHEMBL1235228
DrugBankDB01819
ZINCZINC000003870145
PDB chain5jvl Chain B 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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PDB5jvl Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		R562 R619 M746 E748 G769 N771 D772 C834
Binding residue
(residue number reindexed from 1)		R208 R265 M392 E394 G415 N417 D418 C480
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R338 H456 E748 S767 D772 C834 Y854
Catalytic site (residue number reindexed from 1) R32 H125 E394 S413 D418 C480 Y500
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
View graph for
Cellular Component
External links
PDB RCSB:5jvl, PDBe:5jvl, PDBj:5jvl
PDBsum5jvl
PubMed28358005
UniProtP22221|PPDK_FLATR Pyruvate, phosphate dikinase, chloroplastic (Gene Name=PPDK)

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