Structure of PDB 3ssn Chain D Binding Site BS01

Receptor Information
>3ssn Chain D (length=393) Species: 28040 (Micromonospora griseorubida) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPS
NDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTE
LLRELFGVTHERPAGVRGTKLFPYLTDDEEAVEQIGTYLLAAQQGTEAVL
AGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIG
VGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQN
DAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIED
MWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVD
RNIVGLHVYHNVAFVEKGRNDEGGIPTWIPRDFESLVQASSGG
Ligand information
Ligand IDMVI
InChIInChI=1S/C35H57NO11/c1-9-27-24(18-43-34-32(42)31(41)29(39)23(6)45-34)12-10-11-13-26(37)20(3)16-21(4)33(19(2)14-15-28(38)46-27)47-35-30(40)25(36(7)8)17-22(5)44-35/h10-15,19-25,27,29-35,39-42H,9,16-18H2,1-8H3/b12-10+,13-11+,15-14+/t19-,20+,21-,22+,23+,24+,25-,27+,29+,30+,31+,32+,33+,34+,35-/m0/s1
InChIKeyORPUAOXOPLNKNG-GEUQSOIWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CCC1C(C=CC=CC(=O)C(CC(C(C(C=CC(=O)O1)C)OC2C(C(CC(O2)C)N(C)C)O)C)C)COC3C(C(C(C(O3)C)O)O)O
OpenEye OEToolkits 1.7.2CC[C@@H]1[C@H](/C=C/C=C/C(=O)[C@@H](C[C@@H]([C@@H]([C@H](/C=C/C(=O)O1)C)O[C@H]2[C@@H]([C@H](C[C@H](O2)C)N(C)C)O)C)C)CO[C@H]3[C@@H]([C@@H]([C@@H]([C@H](O3)C)O)O)O
CACTVS 3.370CC[CH]1OC(=O)C=C[CH](C)[CH](O[CH]2O[CH](C)C[CH]([CH]2O)N(C)C)[CH](C)C[CH](C)C(=O)C=CC=C[CH]1CO[CH]3O[CH](C)[CH](O)[CH](O)[CH]3O
CACTVS 3.370CC[C@H]1OC(=O)\C=C\[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@@H]([C@H]2O)N(C)C)[C@@H](C)C[C@@H](C)C(=O)/C=C/C=C/[C@@H]1CO[C@@H]3O[C@H](C)[C@@H](O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=C3C=CC=CC(COC1OC(C(O)C(O)C1O)C)C(OC(=O)C=CC(C)C(OC2OC(C)CC(N(C)C)C2O)C(C)CC3C)CC
FormulaC35 H57 N O11
NameMycinamicin VI;
[(2R,3R,4E,6E,9R,11S,12S,13S,14E)-2-ethyl-9,11,13-trimethyl-8,16-dioxo-12-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}oxacyclohexadeca-4,6,14-trien-3-yl]methyl 6-deoxy-beta-D-allopyranoside
ChEMBL
DrugBank
ZINCZINC000087528535
PDB chain3ssn Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3ssn A new structural form in the SAM/metal-dependent o‑methyltransferase family: MycE from the mycinamicin biosynthetic pathway.
Resolution2.392 Å
Binding residue
(original residue number in PDB)		I383 L390 S394
Binding residue
(residue number reindexed from 1)		I379 L386 S390
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.238: mycinamicin VI 2''-O-methyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0008168 methyltransferase activity
GO:0008171 O-methyltransferase activity
GO:0046872 metal ion binding
GO:0102302 mycinamicin VI 2''-O-methyltransferase activity
Biological Process
GO:0017000 antibiotic biosynthetic process
GO:0032259 methylation
GO:0051289 protein homotetramerization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3ssn, PDBe:3ssn, PDBj:3ssn
PDBsum3ssn
PubMed21884704
UniProtQ83WF2|MYCE_MICGR Mycinamicin VI 2''-O-methyltransferase (Gene Name=mycE)

[Back to BioLiP]