Structure of PDB 7wpn Chain A Binding Site BS01

Receptor Information
>7wpn Chain A (length=478) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGTDE
HGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEERHK
HVVEQVFERLLKQGDIYLGEYLVKEESYFFNISKYTDRLLEFYDQNPDFI
QPPSRKNEMINNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALV
NYISALGYLSDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPL
PKKVFAHGWILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFG
SDGVFTPEAFVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHE
LDEEMEAMALETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWV
LAKDDSQKDMLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQ
FMEFSSLEQYGVLNESIMVTGQPKPIFP
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain7wpn Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7wpn Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y13 H20 G22 H23 S26 A270 E272 H299 W301 I302 K308 S310 K311
Binding residue
(residue number reindexed from 1)		Y11 H18 G20 H21 S24 A228 E230 H257 W259 I260 K266 S268 K269
Annotation score5
Enzymatic activity
Enzyme Commision number 6.1.1.10: methionine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004825 methionine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006431 methionyl-tRNA aminoacylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7wpn, PDBe:7wpn, PDBj:7wpn
PDBsum7wpn
PubMed35474479
UniProtQ5HII6|SYM_STAAC Methionine--tRNA ligase (Gene Name=metG)

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