Structure of PDB 7r3b Chain D Binding Site BS01

Receptor Information
>7r3b Chain D (length=369) Species: 1590 (Lactiplantibacillus plantarum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RHLFTSESVSEGHPDKIADQISDAILDAMLAQDPQARVAVETSVTTGLVL
VFGEVSTKAYVDIQKVVRDTIKSIGYVDGQYGFDGDNCAVLVSLDEQSIG
AGDQGMMFGYAINETPELMPLPIALSHRLMRKIAALRKDGTIKWLRPDAK
AQVTVEYDEDNQPKRIDTVVLSTQHDPDVDLDTIRQTVIDQVIKAVLPAD
LLDDQTKYLVNPTGRFVIGGPQGDAGLTGRKVIVDTYGGFAHHGGGAFSG
KDATKVDRSASYAARYIAKNVVAAGLADQVEVQLAYAIGVAEPVSIAVDT
AGTGKVSDEALINAIRENFDLRPAGIIKMLDLQRPIYRQTAAYGHFGRTD
IDLPWEHTDKVDALKAAFK
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain7r3b Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7r3b Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains.
Resolution2.82 Å
Binding residue
(original residue number in PDB)		H16 P17 D18 D174 K176 D250 R256 K257
Binding residue
(residue number reindexed from 1)		H13 P14 D15 D148 K150 D224 R230 K231
Annotation score3
Enzymatic activity
Enzyme Commision number 2.5.1.6: methionine adenosyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004478 methionine adenosyltransferase activity
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:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7r3b, PDBe:7r3b, PDBj:7r3b
PDBsum7r3b
PubMed35762725
UniProtQ88XB8|METK_LACPL S-adenosylmethionine synthase (Gene Name=metK)

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