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Structure of PDB 6vd0 Chain D Binding Site BS02

Receptor Information >6vd0 Chain D (length=388) 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 NLDLKRGGNGRFQKTAAYGHFGRDDPDFTWEVVKPLKW

Ligand information Ligand ID APC InChI InChI=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 InChIKey CAWZRIXWFRFUQB-IOSLPCCCSA-N SMILES Software SMILES OpenEye OEToolkits 1.5.0 c1nc(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 3.341 Nc1ncnc2n(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 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N ACDLabs 10.04 O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O Formula C11 H18 N5 O12 P3 Name DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER; ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE ChEMBL CHEMBL132722 DrugBank DB02596 ZINC ZINC000008295117 PDB chain 6vd0 Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure 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] PDB 6vd0 S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Resolution 2.0 Å Binding residue (original residue number in PDB) H15 P16 D17 D167 K169 S235 R237 F238 D246 R252 K253 Binding residue (residue number reindexed from 1) H15 P16 D17 D167 K169 S235 R237 F238 D246 R252 K253 Annotation score 3

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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