Structure of PDB 3m2d Chain A Binding Site BS01

Receptor Information
>3m2d Chain A (length=291) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHT
SGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWIS
SGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADY
VRTFFQRLNMNDREVVALMGAHALGKTHLKRSGYEGPWGAANNVFTNEFY
LNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYAN
DQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL
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 chain3m2d Chain A Residue 296 [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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PDB3m2d Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		R48 W51 P145 D146 A147 F158 L171 M172 A174 H175 G178 K179 T180 H181 R184 S185 W191 L232
Binding residue
(residue number reindexed from 1)		R45 W48 P142 D143 A144 F155 L168 M169 A171 H172 G175 K176 T177 H178 R181 S182 W188 L229
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R48 H52 H175 W191 D235
Catalytic site (residue number reindexed from 1) R45 H49 H172 W188 D232
Enzyme Commision number 1.11.1.5: cytochrome-c peroxidase.
Gene Ontology
Molecular Function
GO:0004601 peroxidase activity
GO:0020037 heme binding
Biological Process
GO:0006979 response to oxidative stress
GO:0034599 cellular response to oxidative stress

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3m2d, PDBe:3m2d, PDBj:3m2d
PDBsum3m2d
PubMed20230048
UniProtP00431|CCPR_YEAST Cytochrome c peroxidase, mitochondrial (Gene Name=CCP1)

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