Structure of PDB 3axm Chain B Binding Site BS02

Receptor Information
>3axm Chain B (length=443) Species: 39947 (Oryza sativa Japonica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFKAGVKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG
TWTTVWTDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVT
NMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNK
YGRPLLGCTIKPKLGLSAKNYGRACYECLRGGLDFTKDDENVNSQPFMRW
RDRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPI
VMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVL
AKALRMSGGDHIHAGTVEREMTLGFVDLLRDDFIEKDRARGIFFTQDWVS
MPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAAN
RVALEACVQARNEGRDLAREGNEIIRSACKWSPELAAACEIWK
Ligand information
Ligand ID6PG
InChIInChI=1S/C6H13O10P/c7-2(1-16-17(13,14)15)3(8)4(9)5(10)6(11)12/h2-5,7-10H,1H2,(H,11,12)(H2,13,14,15)/t2-,3-,4+,5-/m1/s1
InChIKeyBIRSGZKFKXLSJQ-SQOUGZDYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
OpenEye OEToolkits 1.5.0C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(O)C(O)C(=O)O
OpenEye OEToolkits 1.5.0C(C(C(C(C(C(=O)O)O)O)O)O)OP(=O)(O)O
CACTVS 3.341O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH](O)C(O)=O
FormulaC6 H13 O10 P
Name6-PHOSPHOGLUCONIC ACID
ChEMBLCHEMBL1230513
DrugBankDB02076
ZINCZINC000001532623
PDB chain3axm Chain B Residue 479 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3axm Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
Resolution1.65 Å
Binding residue
(original residue number in PDB)		K175 K201 R295 H298 S379
Binding residue
(residue number reindexed from 1)		K161 K187 R281 H284 S359
Annotation score2
Binding affinityMOAD: Ki=8.5uM
PDBbind-CN: -logKd/Ki=5.07,Ki=8.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) D203 E204 H294 H327
Catalytic site (residue number reindexed from 1) D189 E190 H280 H313
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3axm, PDBe:3axm, PDBj:3axm
PDBsum3axm
PubMed22609438
UniProtP0C512|RBL_ORYSJ Ribulose bisphosphate carboxylase large chain (Gene Name=rbcL)

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