Structure of PDB 6bdy Chain A Binding Site BS01

Receptor Information
>6bdy Chain A (length=326) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPF
FMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVG
LFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPK
LSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFA
EYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKAT
IWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV
EDYARRKGMSVTEVERWLAPNLGYDA
Ligand information
Ligand IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain6bdy Chain A Residue 1301 [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]
PDB6bdy Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.
Resolution1.512 Å
Binding residue
(original residue number in PDB)		D946 R1134 P1135 A1136 Y1139 P1140 A1141 Y1189
Binding residue
(residue number reindexed from 1)		D46 R234 P235 A236 Y239 P240 A241 Y289
Annotation score1
Binding affinityMOAD: Kd=2.04uM
PDBbind-CN: -logKd/Ki=5.69,Kd=2.04uM
Enzymatic activity
Enzyme Commision number 2.1.1.13: methionine synthase.
Gene Ontology
Molecular Function
GO:0008705 methionine synthase activity
Biological Process
GO:0009086 methionine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6bdy, PDBe:6bdy, PDBj:6bdy
PDBsum6bdy
PubMed29733595
UniProtP13009|METH_ECOLI Methionine synthase (Gene Name=metH)

[Back to BioLiP]