Structure of PDB 8bdb Chain E Binding Site BS02

Receptor Information
>8bdb Chain E (length=468) Species: 42003 (Griffithsia monilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYESGVIPYAKMGYWDPNYAVKDTDILALFRVSPQPGVDPVEASAAVAGE
SSTATWTVVWTDLLTACDLYRAKAYKVESVPNTSDQYFAYISYDIDLFEE
GSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGIVVERE
RMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINSQP
FMRWKERFLYSIEAVNRSIAATGEVKGHYMNVTAATMEEMYERAEFAKQL
GTVIIMIDLVIGYTAIQTMGIWARKNDMILHLHRAGNSTYSRQKIHGMNF
RVICKWMRMAGVDHIHAGTVVGKLEGDPLMIRGFYNTLLLPYLEVNLPQG
IFFQQDWASLRKVTPVASGGIHCGQMHQLLDYLGNDVVLQFGGGTIGHPD
GIQAGATANRVALESMVIARNEGRDYVAEGPQILRDAAKTCGPLQTALDL
WKDITFNYTSTDTADFVE
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 chain8bdb Chain E Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8bdb Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		T177 K179 K205 D207 E208 H297 R298 H330 K337 L338 S382 G383 G406 G407
Binding residue
(residue number reindexed from 1)		T163 K165 K191 D193 E194 H283 R284 H316 K323 L324 S368 G369 G392 G393
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8bdb, PDBe:8bdb, PDBj:8bdb
PDBsum8bdb
PubMed37291398
UniProtA7UM67

[Back to BioLiP]