Structure of PDB 1pfy Chain A Binding Site BS02

Receptor Information
>1pfy 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 IDMSP
InChIInChI=1S/C15H25N7O7S2/c1-30-3-2-7(16)14(25)21-31(26,27)28-4-8-10(23)11(24)15(29-8)22-6-20-9-12(17)18-5-19-13(9)22/h5-8,10-11,13,15,23-24H,2-4,16-17H2,1H3,(H,18,19)(H,21,25)/t7-,8+,10+,11+,13?,15+/m0/s1
InChIKeySQDXXTAOGLOMRP-VOLIQSIHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCCC(C(=O)NS(=O)(=O)OCC1C(C(C(O1)N2C=NC3=C(NC=NC32)N)O)O)N
OpenEye OEToolkits 1.5.0CSCC[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(NC=NC32)N)O)O)N
CACTVS 3.341CSCC[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=NC3=C(N)NC=N[C@H]23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(N2C=NC1=C(N)NC=NC12)C(O)C3O)C(N)CCSC
CACTVS 3.341CSCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=NC3=C(N)NC=N[CH]23
FormulaC15 H25 N7 O7 S2
Name5'-O-[(L-METHIONYL)-SULPHAMOYL]ADENOSINE
ChEMBL
DrugBankDB02229
ZINC
PDB chain1pfy 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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PDB1pfy Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		A12 L13 Y15 G23 H24 E27 D52 W253 A256 P257 Y260 G294 D296 I297 H301 Y325 V326
Binding residue
(residue number reindexed from 1)		A9 L10 Y12 G20 H21 E24 D49 W250 A253 P254 Y257 G291 D293 I294 H298 Y322 V323
Annotation score1
Binding affinityMOAD: ic50~7nM
PDBbind-CN: -logKd/Ki=8.15,IC50=7nM
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:1pfy, PDBe:1pfy, PDBj:1pfy
PDBsum1pfy
PubMed12946347
UniProtP00959|SYM_ECOLI Methionine--tRNA ligase (Gene Name=metG)

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