Structure of PDB 6vdq Chain A Binding Site BS01

Receptor Information
>6vdq Chain A (length=305) Species: 1914 (Streptomyces lavendulae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VAQVATVPFRLGRPEELPGTLDELRAAVSARAGEAVRGLNRPGARTDLAA
LLAATERTRAALAPVGAGPVGDDPSESEANRDNDLAFGIVRTRGPVAELL
VDAALAALAGILEVAVDRGSDLEDAAWQRFIGGFDALLGWLADPHSAPRP
ATVPGAGPAGPPVHQDALRRWVRGHHVFMVLAQGCALATACLRDSAARGD
LPGAEASAAAAEALMRGCQGALLYAGDANREQYNEQIRPTLMPPVAPPKM
SGLHWRDHEVLIKELAGSRDAWEWLSAQGSERPATFRAALAETYDSHIGV
CGHFV
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 chain6vdq Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vdq A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis -His ligand set revealed by a de novo crystal structural and spectroscopic study.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		F194 C234 M266 W271 H274 I278 H313 C317 F320
Binding residue
(residue number reindexed from 1)		F178 C218 M250 W255 H258 I262 H297 C301 F304
Annotation score1
Enzymatic activity
Enzyme Commision number 1.11.2.5: 3-methyl-L-tyrosine peroxygenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:6vdq, PDBe:6vdq, PDBj:6vdq
PDBsum6vdq
PubMed34163669
UniProtB0CN28|SFMD_STRLA 3-methyl-L-tyrosine peroxygenase (Gene Name=sfmD)

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