Structure of PDB 1upm Chain R Binding Site BS03

Receptor Information
>1upm Chain R (length=467) Species: 3562 (Spinacia oleracea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVA
AESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLF
EEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVE
RDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS
QPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFAR
ELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHG
MHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDR
SRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLG
HPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAA
CEVWKEIKFEFPAMDTV
Ligand information
Ligand IDCAP
InChIInChI=1S/C6H14O13P2/c7-3(1-18-20(12,13)14)4(8)6(11,5(9)10)2-19-21(15,16)17/h3-4,7-8,11H,1-2H2,(H,9,10)(H2,12,13,14)(H2,15,16,17)/t3-,4-,6-/m1/s1
InChIKeyITHCSGCUQDMYAI-ZMIZWQJLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C(C(C(COP(=O)(O)O)(C(=O)O)O)O)O)OP(=O)(O)O
CACTVS 3.341O[CH](CO[P](O)(O)=O)[CH](O)[C](O)(CO[P](O)(O)=O)C(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(O)(C(=O)O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0C([C@H]([C@H]([C@](COP(=O)(O)O)(C(=O)O)O)O)O)OP(=O)(O)O
CACTVS 3.341O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@](O)(CO[P](O)(O)=O)C(O)=O
FormulaC6 H14 O13 P2
Name2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain1upm Chain V Residue 477 [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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PDB1upm Calcium Supports Loop Closure But not Catalysis in Rubisco
Resolution2.3 Å
Binding residue
(original residue number in PDB)		E60 T65 W66 N123
Binding residue
(residue number reindexed from 1)		E52 T57 W58 N115
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) D203 E204 H294 H327 K334
Catalytic site (residue number reindexed from 1) D195 E196 H286 H319 K326
Enzyme Commision number 4.1.1.39: ribulose-bisphosphate carboxylase.
Gene Ontology
Molecular Function
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1upm, PDBe:1upm, PDBj:1upm
PDBsum1upm
PubMed14596800
UniProtP00875|RBL_SPIOL Ribulose bisphosphate carboxylase large chain (Gene Name=rbcL)

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