Structure of PDB 7wpx Chain A Binding Site BS01

Receptor Information
>7wpx Chain A (length=519) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGTD
EHGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEERH
KHVVEQVFERLLKQGDIYLGEYEGWYSVPDETYYTESQLVDPQYENGKII
GGKSPDSGHEVELVKEESYFFNISKYTDRLLEFYDQNPDFIQPPSRKNEM
INNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALVNYISALGYL
SDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPLPKKVFAHGW
ILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFGSDGVFTPEA
FVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHELDEEMEAMA
LETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWVLAKDDSQKD
MLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQFMEFSSLEQ
YGVLNESIMVTGQPKPIFP
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 chain7wpx 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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PDB7wpx 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 Y14 H20 G22 H23 S26 K56 A270 E272 H299 W301 I302 K308 K311 S312
Binding residue
(residue number reindexed from 1)		Y12 Y13 H19 G21 H22 S25 K55 A269 E271 H298 W300 I301 K307 K310 S311
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:7wpx, PDBe:7wpx, PDBj:7wpx
PDBsum7wpx
PubMed35474479
UniProtQ5HII6|SYM_STAAC Methionine--tRNA ligase (Gene Name=metG)

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