Structure of PDB 6xub Chain B Binding Site BS01

Receptor Information
>6xub Chain B (length=231) Species: 1717 (Corynebacterium diphtheriae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNFEELNSMQRYSQFAVFRAIPGALGSDRAEIVAQAQSFFDGLETAGKVE
VRGIYDLAGCRAEADFMIWWIAEEFEEIQAAFARFRRETVLGQVSEVAWL
GNSLHRPAEFNRSHLPSFIMGEIPGDWITVYPFVRSYDWYIMDPQKRRKI
LAEHGQAARDFPDVRANTVPAFALGDYEWMLAFEAPRLDRIVDLMHKMRY
TEARLHVREETPFFTGRRVSEVSELVNVLPG
Ligand information
Ligand IDVOV
InChIInChI=1S/C35H36N4O6.Fe/c1-6-21-17(2)25-13-26-18(3)23(8-11-34(42)43)31(37-26)16-32-24(9-12-35(44)45)20(5)28(39-32)15-30-22(7-10-33(40)41)19(4)27(38-30)14-29(21)36-25;/h6,13-16H,1,7-12H2,2-5H3,(H5,36,37,38,39,40,41,42,43,44,45);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyWHUQBNXBFVNCIJ-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)CCC(=O)O)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N]5C(=CC6=NC(=Cc4c(C)c3CCC(O)=O)C(=C6C=C)C)C(=C(CCC(O)=O)C5=CC1=N2)C
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N@]5C(=CC6=NC(=Cc4c(C)c3CCC(O)=O)C(=C6C=C)C)C(=C(CCC(O)=O)C5=CC1=N2)C
FormulaC35 H34 Fe N4 O6
Nameharderoheme (III)
ChEMBL
DrugBank
ZINC
PDB chain6xub Chain B 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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PDB6xub Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		F114 N115 H118 Y135 F137 R139 W143 H158 A162 W183 L185 F187 L198 M199 R208
Binding residue
(residue number reindexed from 1)		F110 N111 H114 Y131 F133 R135 W139 H154 A158 W179 L181 F183 L194 M195 R204
Annotation score4
Enzymatic activity
Enzyme Commision number 1.3.98.5: hydrogen peroxide-dependent heme synthase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016634 oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0006783 heme biosynthetic process
GO:0006785 heme B biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6xub, PDBe:6xub, PDBj:6xub
PDBsum6xub
PubMed32440366
UniProtQ6NGV6

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