Structure of PDB 6spn Chain A Binding Site BS03

Receptor Information
>6spn Chain A (length=544) 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
AFLNTELTWDGIQQPLLGHKVNPFKALYNRIDMRQVEALVEASK
Ligand information
Ligand IDB3M
InChIInChI=1S/C6H13NO2S/c1-10-3-2-5(7)4-6(8)9/h5H,2-4,7H2,1H3,(H,8,9)/t5-/m0/s1
InChIKeyQWVNCDVONVDGDV-YFKPBYRVSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CSCC[CH](N)CC(O)=O
ACDLabs 10.04O=C(O)CC(N)CCSC
OpenEye OEToolkits 1.5.0CSCC[C@@H](CC(=O)O)N
CACTVS 3.341CSCC[C@H](N)CC(O)=O
OpenEye OEToolkits 1.5.0CSCCC(CC(=O)O)N
FormulaC6 H13 N O2 S
Name(3R)-3-amino-5-(methylsulfanyl)pentanoic acid
ChEMBL
DrugBank
ZINCZINC000002386818
PDB chain6spn Chain A Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6spn Use of beta3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		K217 K295 D296 Y325 I367
Binding residue
(residue number reindexed from 1)		K214 K292 D293 Y322 I364
Annotation score2
Binding affinityMOAD: Kd=1.2mM
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:6spn, PDBe:6spn, PDBj:6spn
PDBsum6spn
PubMed31862305
UniProtP00959|SYM_ECOLI Methionine--tRNA ligase (Gene Name=metG)

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