Structure of PDB 1pfv Chain A Binding Site BS02

Receptor Information
>1pfv Chain A (length=547) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRMRGHEVNFICADDA
HGTPIMLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENR
QLSELIYSRLKENGFIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQ
YGDNCEVCGATYSPTELIEPKSVVSGATPVMRDSEHFFFDLPSFSEMLQA
WTRSGALQEQVANKMQEWFESGLQQWDISRDAPYFGFEIPNAPGKYFYVW
LDAPIGYMGSFKNLCDKRGDSVSFDEYWKKDSTAELYHFIGKDIVYFHSL
FWPAMLEGSNFRKPSNLFVHGYVTVNGAKMSKSRGTFIKASTWLNHFDAD
SLRYYYTAKLSSRIDDIDLNLEDFVQRVNADIVNKVVNLASRNAGFINKR
FDGVLASELADPQLYKTFTDAAEVIGEAWESREFGKAVREIMALADLANR
YVDEQAPWVVAKQEGRDADLQAICSMGINLFRVLMTYLKPVLPKLTERAE
AFLNTELTWDGIQQPLLGHKVNPFKALYNRIDMRQVEALVEASKEEV
Ligand information
Ligand ID2FM
InChIInChI=1S/C5H9F2NO2S/c6-5(7)11-2-1-3(8)4(9)10/h3,5H,1-2,8H2,(H,9,10)/t3-/m0/s1
InChIKeyYHBNXKYHZMAFED-VKHMYHEASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CSC(F)F)[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCSC(F)F)C(O)=O
CACTVS 3.341N[CH](CCSC(F)F)C(O)=O
OpenEye OEToolkits 1.5.0C(CSC(F)F)C(C(=O)O)N
ACDLabs 10.04FC(F)SCCC(C(=O)O)N
FormulaC5 H9 F2 N O2 S
NameS-(DIFLUOROMETHYL)HOMOCYSTEINE;
DIFLUOROMETHIONINE
ChEMBL
DrugBankDB03816
ZINC
PDB chain1pfv Chain A Residue 553 [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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PDB1pfv Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		A12 L13 Y15 D52 W253 A256 P257 Y260
Binding residue
(residue number reindexed from 1)		A9 L10 Y12 D49 W250 A253 P254 Y257
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) L13 H21 H24 D52 D129 K132 S175 S178 K332 K335
Catalytic site (residue number reindexed from 1) L10 H18 H21 D49 D126 K129 S172 S175 K329 K332
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:1pfv, PDBe:1pfv, PDBj:1pfv
PDBsum1pfv
PubMed12946347
UniProtP00959|SYM_ECOLI Methionine--tRNA ligase (Gene Name=metG)

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