Structure of PDB 3ofk Chain A Binding Site BS01

Receptor Information
>3ofk Chain A (length=204) Species: 133505 (Bradyrhizobium sp. WM9) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPFTMVSVDNTYQSLERELANDDPWRLDDNPFERERHTQLLRLSLSSGAV
SNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWA
ATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVF
GSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARF
RNPE
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 chain3ofk Chain A Residue 217 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ofk Crystal Structures of NodS N-Methyltransferase from Bradyrhizobium japonicum in Ligand-Free Form and as SAH Complex.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		L10 W20 L22 R31 H32 G52 A54 D73 V74 D98 I99 A114 V116
Binding residue
(residue number reindexed from 1)		L15 W25 L27 R36 H37 G57 A59 D78 V79 D103 I104 A119 V121
Annotation score4
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
Biological Process
GO:0009312 oligosaccharide biosynthetic process
GO:0009877 nodulation
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3ofk, PDBe:3ofk, PDBj:3ofk
PDBsum3ofk
PubMed20970431
UniProtQ9AQ22

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