Structure of PDB 2yiu Chain D Binding Site BS01

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 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 chain2yiu Chain D Residue 500 [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]
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)		Q58 G62 I63 V66 R94 H97 A98 T142 G146 Y147 L149 H198 Y199 P202
Binding residue
(residue number reindexed from 1)		Q56 G60 I61 V64 R92 H95 A96 T140 G144 Y145 L147 H196 Y197 P200
Annotation score1
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

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

[Back to BioLiP]