Structure of PDB 4ndn Chain A Binding Site BS01

Receptor Information
>4ndn Chain A (length=362) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGM
ILLAGEITSRAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQS
PQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQ
VTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPA
KYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFS
GKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIF
HYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRD
SFPWEVPKKLKY
Ligand information
Ligand IDPPK
InChIInChI=1S/H6NO9P3/c2-11(3,4)1-12(5,6)10-13(7,8)9/h(H2,7,8,9)(H4,1,2,3,4,5,6)
InChIKeyPELPUMGXMYVGSQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OP(=O)(O)O)(O)NP(=O)(O)O
OpenEye OEToolkits 1.5.0N(P(=O)(O)O)P(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0N(P(=O)(O)O)[P@](=O)(O)OP(=O)(O)O
CACTVS 3.341O[P](O)(=O)N[P@@](O)(=O)O[P](O)(O)=O
FormulaH6 N O9 P3
Name(DIPHOSPHONO)AMINOPHOSPHONIC ACID
ChEMBL
DrugBankDB03075
ZINC
PDB chain4ndn Chain A Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ndn Structure and function study of the complex that synthesizes S-adenosylmethionine.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		E23 H29 D31 K181 R264 K265
Binding residue
(residue number reindexed from 1)		E9 H15 D17 K148 R231 K232
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H29 D31 K32 E57 E70 K181 F250 D258 A259 R264 K265 K285 K289 D291
Catalytic site (residue number reindexed from 1) H15 D17 K18 E43 E56 K148 F217 D225 A226 R231 K232 K252 K256 D258
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:0036094 small molecule binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006556 S-adenosylmethionine biosynthetic process
GO:0006730 one-carbon metabolic process
GO:0034214 protein hexamerization
GO:0051291 protein heterooligomerization
GO:0061431 cellular response to methionine
GO:1904263 positive regulation of TORC1 signaling
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005829 cytosol
GO:0048269 methionine adenosyltransferase complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ndn, PDBe:4ndn, PDBj:4ndn
PDBsum4ndn
PubMed25075345
UniProtP31153|METK2_HUMAN S-adenosylmethionine synthase isoform type-2 (Gene Name=MAT2A)

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