Structure of PDB 6vd2 Chain A Binding Site BS02

Receptor Information
>6vd2 Chain A (length=394) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
METFLFTSESVNEGHPDKLCDQISDAVLDACLEQDPDSKVACETCTKTNM
VMVFGEITTKATIDYEKIVRDTCRSIGFISDDVGLDADKCKVLVNIEQQS
PDIAQGVHGHFTKRPEDIGAGDQGHMFGYATDETPELMPLSHVLATKIGA
RLTEVRKNGTCRWLRPDGKTQVTVEYYNDNGAMVPVRVHTVLISTQHDET
VTNDEIARDLKEHVIKPIIPEKYLDDKTIFHLNPSGRFVIGGPHGDAGLT
GRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSVVANGMAR
RALVQVSYAIGVPEPLSVFVDTYGTGLIPDKEILKIVKETFDFRPGMMTI
NLDLKRGGNGRFQKTAAYGHFGRDDPDFTWEVVKPLKWDKPQLN
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain6vd2 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vd2 S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		E56 Q99 D102 I103 D122 K277 I310
Binding residue
(residue number reindexed from 1)		E56 Q99 D102 I103 D122 K277 I310
Annotation score5
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 K169 F238 D246 A247 R252 K253 K273 K277 D279
Enzyme Commision number 2.5.1.6: methionine adenosyltransferase.
Gene Ontology
Molecular Function
GO:0004478 methionine adenosyltransferase activity
GO:0005507 copper ion binding
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
Cellular Component
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009505 plant-type cell wall
GO:0009506 plasmodesma
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vd2, PDBe:6vd2, PDBj:6vd2
PDBsum6vd2
PubMed32057875
UniProtP17562|METK2_ARATH S-adenosylmethionine synthase 2 (Gene Name=SAM2)

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