Structure of PDB 2yk3 Chain C Binding Site BS01

Receptor Information
>2yk3 Chain C (length=110) Species: 5656 (Crithidia fasciculata) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARAPLPPGDAARGEKLFKGRAAQCHTANQGGANGVGPNLYGLVGRHSGTI
EGYAYSKANAESGVVWTPDVLDVYLENPKKFMPGTKMSFAGMKKPQERAD
VIAYLETLKG
Ligand information
Ligand IDHEC
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,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
InChIKeyHXQIYSLZKNYNMH-LJNAALQVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
OpenEye OEToolkits 1.5.0CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
CACTVS 3.341C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
CACTVS 3.341CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
FormulaC34 H34 Fe N4 O4
NameHEME C
ChEMBL
DrugBank
ZINC
PDB chain2yk3 Chain C Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yk3 Structure of a Trypanosomatid Mitochondrial Cytochrome C with Heme Attached Via Only One Thioether Bond and Implications for the Substrate Recognition Requirements of Heme Lyase.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		A25 C28 H29 V39 G40 L46 S51 G52 I54 Y57 Y59 S60 N63 W70 Y78 L79 T89 K90 M91 F93
Binding residue
(residue number reindexed from 1)		A21 C24 H25 V35 G36 L42 S47 G48 I50 Y53 Y55 S56 N59 W66 Y74 L75 T85 K86 M87 F89
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c
GO:0006123 mitochondrial electron transport, cytochrome c to oxygen
Cellular Component
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yk3, PDBe:2yk3, PDBj:2yk3
PDBsum2yk3
PubMed19459937
UniProtP00078|CYC_CRIFA Cytochrome c

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