Structure of PDB 6kmm Chain D Binding Site BS01

Receptor Information
>6kmm Chain D (length=359) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EEQIVPFYGKHQAGITTAHQTYVYFAALDVTAKEKSDIITLFRNWTSLTQ
MLTSGKKEQRNQYLPPQDTGESADLSPSNLTVTFGFGPSFFEKDGKDRFG
LKSKKPKHLAALPAMPNDNLDEKQGGGDICIQVCADDEQVAFHALRNLLN
QAVGTCEVRFVNKGFLSGGKNGETPRNLFGFKDGTGNQSTEDDSLMNSIV
WVQSGEPDWMTGGTYMAFRKIKMFLEIWDRSSLKDQEDTFGRRKSSGAPF
GQKKETDPVKLNQIPSNSHVSLAKSTGKQILRRAFSYTEGLDPKTGYMDA
GLLFISFQKNPDNQFIPMLKALSAKDALNEYTQTIGSALYACPGGCKKGE
YIAQRLLES
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 chain6kmm Chain D 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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PDB6kmm Characterization of dye-decolorizing peroxidase from Bacillus subtilis.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		N181 K186 G188 T189 G190 I225 M227 F244 H273 K278 R286 L306 F308 M322 L326 L332
Binding residue
(residue number reindexed from 1)		N177 K182 G184 T185 G186 I221 M223 F240 H269 K274 R282 L302 F304 M318 L322 L328
Annotation score4
Enzymatic activity
Enzyme Commision number 1.11.1.-
4.98.1.1: protoporphyrin ferrochelatase.
Gene Ontology
Molecular Function
GO:0004325 ferrochelatase activity
GO:0004601 peroxidase activity
GO:0016829 lyase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0033212 iron import into cell
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005576 extracellular region
GO:0005829 cytosol
GO:0005886 plasma membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6kmm, PDBe:6kmm, PDBj:6kmm
PDBsum6kmm
PubMed32971035
UniProtP39597|EFEB_BACSU Deferrochelatase (Gene Name=efeB)

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