Structure of PDB 6vdp Chain A Binding Site BS01

Receptor Information
>6vdp Chain A (length=304) Species: 1914 (Streptomyces lavendulae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQVATVPFRLGRPEELPGTLDELRAAVSARAGEAVRGLNRPGARTDLAAL
LAATERTRAALAPVGAGPVGDDPSESEANRDNDLAFGIVRTRGPVAELLV
DAALAALAGILEVAVDRGSDLEDAAWQRFIGGFDALLGWLADPHSAPRPA
TVPGAGPAGPPVHQDALRRWVRGHHVFMVLAQGCALATACLRDSAARGDL
PGAEASAAAAEALMRGCQGALLYAGDANREQYNEQIRPTLMPPVAPPKMS
GLHWRDHEVLIKELAGSRDAWEWLSAQGSERPATFRAALAETYDSHIGVC
GHFV
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 chain6vdp 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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PDB6vdp 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.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F194 C234 M266 G268 W271 H274 L277 Y310 H313 C317 F320
Binding residue
(residue number reindexed from 1)		F177 C217 M249 G251 W254 H257 L260 Y293 H296 C300 F303
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

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Molecular Function
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Biological Process
External links
PDB RCSB:6vdp, PDBe:6vdp, PDBj:6vdp
PDBsum6vdp
PubMed34163669
UniProtB0CN28|SFMD_STRLA 3-methyl-L-tyrosine peroxygenase (Gene Name=sfmD)

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