Structure of PDB 3axm Chain A Binding Site BS02

Receptor Information
>3axm Chain A (length=444) Species: 39947 (Oryza sativa Japonica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFKAGVTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTW
TTVWTDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNM
FTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYG
RPLLGCTIKPKLGLSAKNYGRACYECLRGGLDFTKDDENVNSQPFMRWRD
RFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVM
HDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAK
ALRMSGGDHIHAGTVVGKEREMTLGFVDLLRDDFIEKDRARGIFFTQDWV
SMPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAA
NRVALEACVQARNEGRDLAREGNEIIRSACKWSPELAAACEIWK
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 A 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)		K159 K185 R279 H282 S360
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) K175 K201 D202 D203 E204 H294 H327 K334
Catalytic site (residue number reindexed from 1) K159 K185 D186 D187 E188 H278 H311 K318
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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