Structure of PDB 5xet Chain C Binding Site BS01

Receptor Information
>5xet Chain C (length=505) Species: 419947 (Mycobacterium tuberculosis H37Ra) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPYYVTTAIAYPNAAPHVGHAYEYIATDAIARFKRLDRYDVRFLTGTDEH
GLKVAQAAAAAGVPTAALARRNSDVFQRMQEALNISFDRFIRTTDADHHE
ASKELWRRMSAAGDIYLDNYSGWYSVRDERFFVESETQLVDGTRLTVETG
TPVTWTEEQTYFFRLSAYTDKLLAHYHANPDFIAPETRRNEVISFVSGGL
DDLSISRTSFDWGVQVPEHPDHVMYVWVDALTNYLTGAGFPDTDSELFRR
YWPADLHMIGKDIIRFHAVYWPAFLMSAGIELPRRIFAHGFLHNRKMSKS
VGNIVDPVALAEALGVDQVRYFLLREVPFGQDGSYSDEAIVTRINTDLAN
ELGNLAQRSLSMVAKNLDGRVPNPGEFADADAALLATADGLLERVRGHFD
AQAMHLALEAIWLMLGDANKYFSVQQPWVLRKSESEADQARFRTTLYVTC
EVVRIAALLIQPVMPESAGKILDLLGQAPNQRSFAAVGVRLTPGTALPPP
TGVFP
Ligand information
Ligand IDME8
InChIInChI=1S/C15H23N6O8PS/c1-31-3-2-7(16)15(24)29-30(25,26)27-4-8-10(22)11(23)14(28-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H,25,26)(H2,17,18,19)/t7-,8+,10+,11+,14+/m0/s1
InChIKeyRZQLXQQLNKBFRX-TWBCTODHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CSCC[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.7.0CSCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
OpenEye OEToolkits 1.7.0CSCC[C@@H](C(=O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
ACDLabs 11.02O=P(OC(=O)C(N)CCSC)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.352CSCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
FormulaC15 H23 N6 O8 P S
Name[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate;
L-methionine-AMP;
methionyl-adenylate
ChEMBL
DrugBank
ZINCZINC000013536715
PDB chain5xet Chain C Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xet Structural characterization of free-state and product-stateMycobacterium tuberculosismethionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism.
Resolution2.38 Å
Binding residue
(original residue number in PDB)
A9 I10 A11 Y12 H18 G20 E24 D49 W228 A231 Y235 G261 D263 I264 H290 F292
Binding residue
(residue number reindexed from 1)
A8 I9 A10 Y11 H17 G19 E23 D48 W227 A230 Y234 G260 D262 I263 H289 F291
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) I10 D49 W228 I264 K299 K302
Catalytic site (residue number reindexed from 1) I9 D48 W227 I263 K296 K299
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
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006431 methionyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:5xet, PDBe:5xet, PDBj:5xet
PDBsum5xet
PubMed30002848
UniProtA5U150

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