Structure of PDB 7dkf Chain O1 Binding Site BS01

Receptor Information
>7dkf Chain O1 (length=379) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLF
LAMHYTSDTTTAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGR
GLYYGSYTFLETWNIGVILLLTVMATAFMGYVLPWGQMSFWGATVITNLL
SAIPYIGTNLVEWIWGGFSVDKATLTRFFAFHFILPFIIMAIAMVHLLFL
HETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALMLLVLFAPDLL
GDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILI
LALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITI
GQLASVLYFLLILVLMPTAGTIENKLLKW
Ligand information
Ligand IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain7dkf Chain O1 Residue 401 [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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PDB7dkf A Dynamic Substrate Pool Revealed by cryo-EM of a Lipid-Preserved Respiratory Supercomplex.
Resolution8.3 Å
Binding residue
(original residue number in PDB)		Q44 I45 G48 L49 L51 A52 Y55 R80 H83 T126 G130 Y131 P134 H182 F183 P186
Binding residue
(residue number reindexed from 1)		Q44 I45 G48 L49 L51 A52 Y55 R80 H83 T126 G130 Y131 P134 H182 F183 P186
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008121 ubiquinol-cytochrome-c reductase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0048039 ubiquinone binding
Biological Process
GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c
GO:0022904 respiratory electron transport chain
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane
GO:0031966 mitochondrial membrane
GO:0045275 respiratory chain complex III

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7dkf, PDBe:7dkf, PDBj:7dkf
PDBsum7dkf
PubMed34913730
UniProtP00157|CYB_BOVIN Cytochrome b (Gene Name=MT-CYB)

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