Structure of PDB 6vcy Chain A Binding Site BS01

Receptor Information
>6vcy Chain A (length=385) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
METFLFTSESVNEGHPDKLCDQISDAVLDACLEQDPDSKVACETCTKTNM
VMVFGEITTKATVDYEKIVRDTCRAIGFVSDDVGLDADKCKVLVNIEQQS
PDIAQGVKCPEEIGAGDQGHMFGYATDETPELMPLSHVLATKLGARLTEV
RKNGTCAWLRPDGKTQVTVEYYNDKGAMVPIRVHTVLISTQHDETVTNDE
IARDLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVIGGPHGDAGLTGRKII
IDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSVVANGMARRALVQ
VSYAIGVPEPLSVFVDTYETGLIPDKEILKIVKESFDFRPGMMTINLDLK
RGGNGRFLKTAAYGHFGRDDPDFTWEVVKPLKWDK
Ligand information
Ligand IDMTA
InChIInChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKeyWUUGFSXJNOTRMR-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSC)N
CACTVS 3.341CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
FormulaC11 H15 N5 O3 S
Name5'-DEOXY-5'-METHYLTHIOADENOSINE
ChEMBLCHEMBL277041
DrugBankDB02282
ZINCZINC000004228245
PDB chain6vcy Chain A Residue 406 [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]
PDB6vcy S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		H15 D167 S235 F238 D246
Binding residue
(residue number reindexed from 1)		H15 D162 S230 F233 D241
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H15 D17 K18 E43 E56 K169 F238 D246 A247 R252 K253 K273 K277 D279
Catalytic site (residue number reindexed from 1) H15 D17 K18 E43 E56 K164 F233 D241 A242 R247 K248 K268 K272 D274
Enzyme Commision number 2.5.1.6: methionine adenosyltransferase.
Gene Ontology
Molecular Function
GO:0004478 methionine adenosyltransferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006556 S-adenosylmethionine biosynthetic process
GO:0006730 one-carbon metabolic process
GO:0009693 ethylene biosynthetic process
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009505 plant-type cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vcy, PDBe:6vcy, PDBj:6vcy
PDBsum6vcy
PubMed32057875
UniProtP23686|METK1_ARATH S-adenosylmethionine synthase 1 (Gene Name=SAM1)

[Back to BioLiP]