Structure of PDB 2yiu Chain D Binding Site BS03

Receptor Information
>2yiu Chain D (length=428) Species: 318586 (Paracoccus denitrificans PD1222) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIPHDHYEPKTGFERWLHRRLPIVSLVYDTLMIPTPKNLNWWWIWGIVLA
FCLVLQIATGIVLVMHYTPHVDLAFASVEHIMRDVNGGYMLRYLHANGAS
LFFLAVYIHIFRGLYYGSYKAPREVTWIVGMLIYLMMMGTAFMGYVLPWG
QMSFWGATVITGLFGAIPGVGEAIQTWLLGGPAVDNPTLNRFFSLHYLLP
FVIAALVVVHIWAFHTTGNNNPTGVEVRRGSKEEAKKDTLPFWPYFVIKD
LFALAVVLVVFFAIVGFMPNYLGHPDNYIEANPLVTPAHIVPEWYFLPFY
AILRAFTADVWVVMLVNWLSFGIIDAKFFGVIAMFGAILVMALVPWLDTS
RVRSGQYRPLFKWWFWLLAVDFVVLMWVGAMPAEGIYPYIALAGSAYWFA
YFLIILPLLGIIEKPDAMPQTIEEDFNA
Ligand information
Ligand IDSMA
InChIInChI=1S/C30H42O7/c1-10-18(2)13-11-12-14-22(33-6)21(5)29(36-9)19(3)15-16-23-20(4)27(31)26-24(34-7)17-25(35-8)28(32)30(26)37-23/h10-14,17,19,21-22,29,32H,15-16H2,1-9H3/b13-11+,14-12?,18-10+/t19-,21+,22-,29-/m0/s1
InChIKeyUZHDGDDPOPDJGM-WPPYOTIYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2C/C=C(\C)/C=C/C=C[C@@H]([C@@H](C)[C@H]([C@@H](C)CCC1=C(C(=O)c2c(cc(c(c2O1)O)OC)OC)C)OC)OC
CACTVS 3.370CO[CH](C=CC=CC(C)=CC)[CH](C)[CH](OC)[CH](C)CCC1=C(C)C(=O)c2c(OC)cc(OC)c(O)c2O1
OpenEye OEToolkits 1.7.2CC=C(C)C=CC=CC(C(C)C(C(C)CCC1=C(C(=O)c2c(cc(c(c2O1)O)OC)OC)C)OC)OC
CACTVS 3.370CO[C@@H](\C=C\C=C\C(C)=C\C)[C@@H](C)[C@@H](OC)[C@@H](C)CCC1=C(C)C(=O)c2c(OC)cc(OC)c(O)c2O1
FormulaC30 H42 O7
NameSTIGMATELLIN A
ChEMBL
DrugBank
ZINC
PDB chain2yiu Chain D Residue 502 [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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PDB2yiu X-Ray Structure of the Dimeric Cytochrome Bc(1) Complex from the Soil Bacterium Paracoccus Denitrificans at 2.7-A Resolution.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		M140 F144 M145 V161 I292 P294 E295 F298 Y302
Binding residue
(residue number reindexed from 1)		M138 F142 M143 V159 I290 P292 E293 F296 Y300
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.89,IC50=130nM
Enzymatic activity
Catalytic site (original residue number in PDB) H217 N221 K251 D252 E295
Catalytic site (residue number reindexed from 1) H215 N219 K249 D250 E293
Enzyme Commision number 1.10.2.2: Transferred entry: 7.1.1.8.
Gene Ontology
Molecular Function
GO:0008121 ubiquinol-cytochrome-c reductase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
Biological Process
GO:0022904 respiratory electron transport chain
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0045275 respiratory chain complex III

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yiu, PDBe:2yiu, PDBj:2yiu
PDBsum2yiu
PubMed21996020
UniProtP05418|CYB_PARDE Cytochrome b (Gene Name=petB)

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