Structure of PDB 7yk5 Chain B Binding Site BS03

Receptor Information
>7yk5 Chain B (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 B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		K179 E208 R298 H330 K337 S382 G383 G406
Binding residue
(residue number reindexed from 1)		K176 E205 R295 H327 K334 S379 G380 G403
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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