Structure of PDB 3axk Chain A Binding Site BS03

Receptor Information
>3axk Chain A (length=434) Species: 39947 (Oryza sativa Japonica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTTVWTDG
LTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGN
VFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCT
IKPKLGLSAKNYGRACYECLRGGLDFTKDDENVNSQPFMRWRDRFVFCAE
AIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGG
FTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGG
DHIHAGTVVEREMTLGFVDLLRDDFIEKDRARGIFFTQDWVSMPGVIPVA
SGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAANRVALEACV
QARNEGRDLAREGNEIIRSACKWSPELAAACEIW
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-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)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain3axk Chain A Residue 480 [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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PDB3axk Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E60 T68 N123 G126 F127
Binding residue
(residue number reindexed from 1)		E41 T45 N100 G103 F104
Annotation score1
Binding affinityMOAD: Ki=70uM
Enzymatic activity
Catalytic site (original residue number in PDB) K175 K201 D202 D203 E204 H294 H327
Catalytic site (residue number reindexed from 1) K152 K178 D179 D180 E181 H271 H304
Enzyme Commision number 4.1.1.39: ribulose-bisphosphate carboxylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004497 monooxygenase activity
GO:0016829 lyase activity
GO:0016984 ribulose-bisphosphate carboxylase activity
GO:0046872 metal ion binding
Biological Process
GO:0009853 photorespiration
GO:0015977 carbon fixation
GO:0015979 photosynthesis
GO:0019253 reductive pentose-phosphate cycle
Cellular Component
GO:0009507 chloroplast
GO:0009536 plastid

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3axk, PDBe:3axk, PDBj:3axk
PDBsum3axk
PubMed22609438
UniProtP0C512|RBL_ORYSJ Ribulose bisphosphate carboxylase large chain (Gene Name=rbcL)

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