Structure of PDB 8bef Chain N Binding Site BS02

Receptor Information
>8bef Chain N (length=488) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFNLFLAVFPEIFIINATFILLIHGVVFSTSKKYDYPPLASNVGWLGLLS
VLITLLLLAAGAPLLTIAHLFWNNLFRRDNFTYFCQIFLLLSTAGTISMC
FDFFDQERFDAFEFIVLILLSTCGMLFMISAYDLIAMYLAIELQSLCFYV
IAASKRKSEFSTEAGLKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAK
ILTGYEITGARSSGIFMGILFIAVGFLFKITAVPFHMWAPDIYEGSPTPV
TAFLSIAPKISIFANILRVFIYGSYGATLQQIFFFCSIASMILGALAAMA
QTKVKRLLAYSSIGHVGYICIGFSCGTIEGIQSLLIGIFIYALMTMDAFA
IVLALRQTRVKYIADLGALAKTNPILAITFSITMFSYAGIPPLAGFCSKF
YLFFAALGCGAYFLALVGVVTSVIGCFYYIRLVKRMFFDTPRTWILYEPM
DRNKSLLLAMTSFFITLFLLYPSPLFSVTHQMALSLYL
Ligand information
Ligand IDUQ5
InChIInChI=1S/C34H50O4/c1-24(2)14-10-15-25(3)16-11-17-26(4)18-12-19-27(5)20-13-21-28(6)22-23-30-29(7)31(35)33(37-8)34(38-9)32(30)36/h14,16,18,20,22H,10-13,15,17,19,21,23H2,1-9H3/b25-16+,26-18+,27-20+,28-22+
InChIKeyNYFAQDMDAFCWPU-UVCHAVPFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
OpenEye OEToolkits 1.5.0CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CCC=C(C)C
CACTVS 3.341COC1=C(OC)C(=O)C(=C(C)C1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
CACTVS 3.341COC1=C(OC)C(=O)C(=C(C)C1=O)C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C
ACDLabs 10.04O=C1C(=C(C(=O)C(OC)=C1OC)C)C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC/C=C(/C)C
FormulaC34 H50 O4
Name2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
ChEMBL
DrugBank
ZINCZINC000058649852
PDB chain8bef Chain Y Residue 202 [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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PDB8bef Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution.
Resolution2.13 Å
Binding residue
(original residue number in PDB)		V244 P245 M248 F296 C297
Binding residue
(residue number reindexed from 1)		V233 P234 M237 F285 C286
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.1.2: NADH:ubiquinone reductase (H(+)-translocating).
Gene Ontology
Molecular Function
GO:0008137 NADH dehydrogenase (ubiquinone) activity
Biological Process
GO:0042773 ATP synthesis coupled electron transport
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0009536 plastid

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8bef, PDBe:8bef, PDBj:8bef
PDBsum8bef
PubMed36585502
UniProtO05000|NU2M_ARATH NADH-ubiquinone oxidoreductase chain 2 (Gene Name=ND2)

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