Structure of PDB 7yk5 Chain D Binding Site BS02

Receptor Information
>7yk5 Chain D (length=481) Species: 2850 (Phaeodactylum tricornutum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVSERTRIKSDRYESGVIPYAKMGYWDAAYAVKNTDVLALFRITPQPGVD
PVEAAAAVAGESSTATWTVVWTDLLTACDRYRAKAYRVDPVPNTTDQYFA
FIAYECDLFEEGSLANLTASIIGNVFGFKAVSALRLEDMRIPHSYLKTFQ
GPATGVIVERERLNKYGIPLLGATVKPKLGLSGKNYGRVVYEGLKGGLDF
LKDDENINSQPFMRWRERFLYCMEGINRASAATGETKGSYLNITAGTMEE
VYKRAEYAKTVGSIVVMIDLVMGYTAIQSAAIWARDNDLILHLHRAGNST
YARQKNHGINFRVICKWMRMCGVDHIHAGTVVGKLEGDPLMIKGFYDTLL
LTHLNVNLPYGIFFEMTWASLRKCMPVASGGIHCGQMHQLVHYLGDDVVL
QFGGGTIGHPDGIQAGATANRVALEAMILARNEGADYFNSDIGPQILRNA
AKTCGPLQTALDLWKDISFNYTSTDTSDFSV
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 chain7yk5 Chain C Residue 501 [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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PDB7yk5 A linker protein from a red-type pyrenoid phase separates with Rubisco via oligomerizing sticker motifs.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		T69 N127
Binding residue
(residue number reindexed from 1)		T66 N124
Annotation score2
Enzymatic activity
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: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:7yk5, PDBe:7yk5, PDBj:7yk5
PDBsum7yk5
PubMed37311001
UniProtQ9TK52|RBL_PHATC Ribulose bisphosphate carboxylase large chain (Gene Name=rbcL)

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