Structure of PDB 5jvl Chain C Binding Site BS01

Receptor Information
>5jvl Chain C (length=859) 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
PKKQLELAVNAVFDSWDLKGTAVNIQSMVFGNMGNTSGTGVLFTRNPSTG
EKKLYGEFLINAQGEDVVAGIRTPEDLGTMETCMPEAYKELVENCEILER
HYKDMMDIEFTVQENRLWMLQCRTGKRTGKGAVRIAVDMVNEGLIDTRTA
IKRVETQHLDQLLHPQFEDPSAYKSHVVATGLPASPGAAVGQVCFSAEDA
ETWHAQGKSAILVRTETSPEDVGGMHAAAGILTARGGMTSHAAVVARGWG
KCCVSGCADIRVNDDMKIFTIGDRVIKEGDWLSLNGTTGEVILGKQLLAP
PAMSNDLEIFMSWADQARRLKVMANADTPNDALTARNNGAQGIGLCRTEH
MFFASDERIKAVRKMIMAVTPEQRKVALDLLLPYQRSDFEGIFRAMDGLP
VTIRLLDPPLHEFLPEGDLEHIVNELAVDTGMSADEIYSKIENLSEVNPM
LGFRGCRLGISYPELTEMQVRAIFQAAVSMTNQGVTVIPEIMVPLVGTPQ
ELRHQISVIRGVAANVFAEMGVTLEYKVGTMIEIPRAALIAEEIGKEADF
FSFGTNDLTQMTFGYSRDDVGKFLQIYLAQGILQHDPFEVIDQKGVGQLI
KMATEKGRAANPSLKVGICGEHGGEPSSVAFFDGVGLDYVSCSPFRVPIA
RLAAAQVIV
Ligand information
Ligand ID6NQ
InChIInChI=1S/C10H16BrN6O11P3/c11-5-7(18)4(1-26-31(24,25)28-30(22,23)16-29(19,20)21)27-10(5)17-3-15-6-8(12)13-2-14-9(6)17/h2-5,7,10,18H,1H2,(H,24,25)(H2,12,13,14)(H4,16,19,20,21,22,23)/t4-,5-,7-,10-/m1/s1
InChIKeyGLCRVGHVCJLAHS-QYYRPYCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3Br
ACDLabs 12.01c12c(c(N)ncn1)ncn2C3OC(COP(=O)(O)OP(O)(NP(O)(O)=O)=O)C(C3Br)O
OpenEye OEToolkits 2.0.4c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)Br)N
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3Br
OpenEye OEToolkits 2.0.4c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)Br)N
FormulaC10 H16 Br N6 O11 P3
Name2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid
ChEMBL
DrugBank
ZINC
PDB chain5jvl Chain C 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)		K25 S93 R95 T108 L110 M243 V244 G279 E324 L335
Binding residue
(residue number reindexed from 1)		K25 S93 R95 T108 L110 M228 V229 G264 E309 L320
Annotation score3
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 R323 H441 E733 S752 D757 C819 Y839
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

View graph for
Molecular Function
View graph for
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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