Structure of PDB 5uv1 Chain A Binding Site BS03

Receptor Information
>5uv1 Chain A (length=508) Species: 2711 (Citrus sinensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIWDHDFLQSLNSNYTDETYKRRAEELKGKVKTAIKDVTEPLDQLELIDN
LQRLGLAYHFEPEIRNILRNIHNHNKDYNWRKENLYATSLEFRLLRQHGY
PVSQEVFSGFKDDKVGFICDDFKGILSLHEASYYSLEGESIMEEAWQFTS
KHLKEMMIDVFVAEQAKRALELPLHWKAPMLEARWFIHVYEKREDKNHLL
LELAKLEFNTLQAIYQEELKDISGWWKDTGLGEKLSFARNRLVASFLWSM
GIAFEPQFAYCRRVLTISIALITVIDDIYDVYGTLDELEIFTDAVARWDI
NYALKHLPGYMKMCFLALYNFVNEFAYYVLKQQDFDMLLSIKHAWLGLIQ
AYLVEAKWYHSKYTPKLEEYLENGLVSITGPLIITISYLSGTNPIIKKEL
EFLESNPDIVHWSSKIFRLQDDLGTSSDVPKSIQCYMHETGASEEVAREH
IKDMMRQMWKKVNAYTADKDSPLTRTTAEFLLNLVRMSHFMYLHGDVGFT
LLFQPIPL
Ligand information
Ligand ID0FV
InChIInChI=1S/C10H19FO7P2/c1-8(2)5-4-6-9(3)10(11)7-17-20(15,16)18-19(12,13)14/h5H,4,6-7H2,1-3H3,(H,15,16)(H2,12,13,14)/b10-9-
InChIKeyBYJNSLXDWGDGAC-KTKRTIGZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)=CCCC(C)=C(F)CO[P](O)(=O)O[P](O)(O)=O
ACDLabs 12.01O=P(O)(O)OP(=O)(OCC(\F)=C(/C)CC\C=C(/C)C)O
OpenEye OEToolkits 1.7.6CC(=CCC/C(=C(/COP(=O)(O)OP(=O)(O)O)\F)/C)C
CACTVS 3.370CC(C)=CCCC(/C)=C(F)/CO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.6CC(=CCCC(=C(COP(=O)(O)OP(=O)(O)O)F)C)C
FormulaC10 H19 F O7 P2
Name(2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate;
2-fluorogeranyl diphosphate
ChEMBL
DrugBank
ZINC
PDB chain5uv1 Chain A Residue 704 [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]
PDB5uv1 Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed by (+)-Limonene Synthase from Citrus sinensis Using Fluorinated Substrate Analogues.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
W315 I336 D343 T446 F484 R485 D488
Binding residue
(residue number reindexed from 1)
W248 I269 D276 T379 F417 R418 D421
Annotation score3
Binding affinityMOAD: Ki=2.4uM
PDBbind-CN: -logKd/Ki=5.62,Ki=2.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) R306 W315 I336 D343 D347 S444 I445 T446 R485 D488 T492 Y565
Catalytic site (residue number reindexed from 1) R239 W248 I269 D276 D280 S377 I378 T379 R418 D421 T425 Y492
Enzyme Commision number 4.2.3.20: (R)-limonene synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0010333 terpene synthase activity
GO:0016829 lyase activity
GO:0034002 (R)-limonene synthase activity
GO:0046872 metal ion binding
Biological Process
GO:0016102 diterpenoid biosynthetic process
Cellular Component
GO:0009507 chloroplast

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5uv1, PDBe:5uv1, PDBj:5uv1
PDBsum5uv1
PubMed28272876
UniProtA0A1C9J6A7|RLC1_CITSI (R)-limonene synthase 1, chloroplastic

[Back to BioLiP]