Structure of PDB 6vd0 Chain B Binding Site BS02

Receptor Information
>6vd0 Chain B (length=389) 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
NLDLKRGGNGRFQKTAAYGHFGRDDPDFTWEVVKPLKWD
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain6vd0 Chain B Residue 401 [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]
PDB6vd0 S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H15 P16 D17 D167 K169 S235 F238 D246 R252 K253
Binding residue
(residue number reindexed from 1)		H15 P16 D17 D167 K169 S235 F238 D246 R252 K253
Annotation score3
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vd0, PDBe:6vd0, PDBj:6vd0
PDBsum6vd0
PubMed32057875
UniProtP17562|METK2_ARATH S-adenosylmethionine synthase 2 (Gene Name=SAM2)

[Back to BioLiP]