Structure of PDB 6mjf Chain B Binding Site BS01

Receptor Information
>6mjf Chain B (length=370) Species: 1314807 (Dendrothele bispora CBS 962.96) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSLIVVGTGIESIGQMTLQALSYIEAASKVFYCVIDPATEAFILTKNKNC
VDLYQYYDNGKSRMDTYTQMAELMLKEVRNGLDVVGVFYGHPGVFVNPSH
RALAIARSEGYQARMLPGVSAEDCLFADLCIDPSNPGCLTYEASDFLIRE
RPVNVHSHLILFQVGCVGIADFNFSGFDNSKFTILVDRLEQEYGPDHTVV
HYIAAMMPHQDPVTDKFTIGQLREPEIAKRVGGVSTFYIPPKARKDINTD
IIRLLEFLPAGKVPDKHTQIYPPNQWEPDVPTLPPYGQNEQAAITRLEAH
APPEEYQPLATSKAMTDVMTKLALDPKALAEYKADHRAFAQSVPDLTPQE
RAALELGDSWAIRCAMKNMP
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6mjf Chain B Residue 500 [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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PDB6mjf Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis.
Resolution2.198 Å
Binding residue
(original residue number in PDB)		Y97 G98 H99 V102 F103 S128 A129 F170 Q171 Y210 I211 A212 G241 V242 S243 T244
Binding residue
(residue number reindexed from 1)		Y89 G90 H91 V94 F95 S120 A121 F162 Q163 Y202 I203 A204 G233 V234 S235 T236
Annotation score4
Binding affinityMOAD: Kd=6.88uM
PDBbind-CN: -logKd/Ki=5.16,Kd=6.88uM
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6mjf, PDBe:6mjf, PDBj:6mjf
PDBsum6mjf
PubMed30204409
UniProtA0A4S8L4Q5|DBIMA_DENBC Methyltransferase/ribosomally synthesized cyclic peptide dendrothelin A precursor dbihMA (Gene Name=dbiMA)

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