Structure of PDB 7oy2 Chain B Binding Site BS02

Receptor Information
>7oy2 Chain B (length=376) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYETLRFIWWLLIGVILVVFMISDGFDMGIGCLLPLVARNDDERRIVINS
VGAHWEGNQVWLILAGGALFAAWPRVYAAAFSGFYVAMILVLCSLFFRPL
AFDYRGKIADARWRKMWDAGLVIGSLVPPVVFGIAFGNLLLGVPFAFTPQ
LRVEYLGSFWQLLTPFPLLCGLLSLGMVILQGGVWLQLKTVGVIHLRSQL
ATKRAALLVMLCFLLAGYWLWVGIDGFVLLAQDANGPSNPLMKLVAVLPG
AWMNNFVESPVLWIFPLLGFFCPLLTVMAIYRGRPGWGFLMASLMQFGVI
FTAGITLFPFVMPSSVSPISSLTLWDSTSSQLTLSIMLVIVLIFLPIVLL
YTLWSYYKMWGRMTTETLRRNENELY
Ligand information
Ligand IDDK8
InChIInChI=1S/C50H70O2/c1-38(2)19-12-20-39(3)21-13-22-40(4)23-14-24-41(5)25-15-26-42(6)27-16-28-43(7)29-17-30-44(8)31-18-32-45(9)35-36-46-37-49(51)47-33-10-11-34-48(47)50(46)52/h10-11,19,21,23,25,27,29,31,33-35,37H,12-18,20,22,24,26,28,30,32,36H2,1-9H3/b39-21+,40-23+,41-25+,42-27+,43-29-,44-31+,45-35+
InChIKeyGDUBPWSFXUAETN-FTDSSYSJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCC1=CC(=O)c2ccccc2C1=O)C)C)C)C)C)C)C)C
CACTVS 3.385CC(C)=CCC\C(C)=C\CCC(/C)=C/CCC(/C)=C/CCC(/C)=C/CCC(\C)=C/CCC(/C)=C/CCC(/C)=C/CC1=CC(=O)c2ccccc2C1=O
OpenEye OEToolkits 2.0.7CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C\CC/C(=C/CC/C(=C/CC1=CC(=O)c2ccccc2C1=O)/C)/C)/C)/C)/C)/C)/C)C
CACTVS 3.385CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=CC(=O)c2ccccc2C1=O
FormulaC50 H70 O2
Name2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]naphthalene-1,4-dione;
demethlymenaquinone-8
ChEMBL
DrugBank
ZINC
PDB chain7oy2 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7oy2 Mechanistic and structural diversity between cytochrome bd isoforms of Escherichia coli .
Resolution2.06 Å
Binding residue
(original residue number in PDB)		W12 G16 L19 F22 M23 V78 A82 F134 F138 L175 S176 F215 G219 L222 M255 F258 W265 P268 I302 F303 T304 T308 V313
Binding residue
(residue number reindexed from 1)		W10 G14 L17 F20 M21 V76 A80 F132 F136 L173 S174 F213 G217 L220 M253 F256 W263 P266 I300 F301 T302 T306 V311
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.1.3: ubiquinol oxidase (H(+)-transporting).
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0009486 cytochrome bo3 ubiquinol oxidase activity
GO:0016682 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0046872 metal ion binding
Biological Process
GO:0006119 oxidative phosphorylation
GO:0019646 aerobic electron transport chain
GO:0055085 transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0070069 cytochrome complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7oy2, PDBe:7oy2, PDBj:7oy2
PDBsum7oy2
PubMed34873041
UniProtP26458|APPB_ECOLI Cytochrome bd-II ubiquinol oxidase subunit 2 (Gene Name=appB)

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