Structure of PDB 8pty Chain C Binding Site BS02

Receptor Information
>8pty Chain C (length=440) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGIAVVAVMCKPHRCPHISFTGNICVYCPGGPDSDFEYSTQSYTGYEPTS
MRAIRARYDPFLQTRHRIEQLKQLGHSVDKVEFIVMGGTFMALPEEYRDY
FIRNLHDALSGHTSNNIYEAVKYSERSLTKCIGITIETRPDYCMKRHLSD
MLTYGCTRLEIGVQSVYEDVARDTNRGHTVKAVCESFHLAKDSGFKVVAH
MMPDLPNVGLERDIEQFTEFFENPAFRPDGLKLYPTLVIRGTGLYELWKS
GRYKSYSPSDLVELVARILALVPPWTRVYRVQRDIPMPLVSSGVEHGNLR
ELALARMKDLGIQCRDVRTREVPYQVELVRRDYVANGGWETFLSYEDPDQ
DILIGLLRLRKCSEETFRFELGGGVSIVRELHVYGSVQGFGMLLMEEAER
IAREEHGSGKIAVISGVGTRNYYRKIGYRLQGPYMVKMLK
Ligand information
Ligand IDMET
InChIInChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
InChIKeyFFEARJCKVFRZRR-BYPYZUCNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CSCC[CH](N)C(O)=O
OpenEye OEToolkits 1.5.0CSCCC(C(=O)O)N
CACTVS 3.341CSCC[C@H](N)C(O)=O
OpenEye OEToolkits 1.5.0CSCC[C@@H](C(=O)O)N
ACDLabs 10.04O=C(O)C(N)CCSC
FormulaC5 H11 N O2 S
NameMETHIONINE
ChEMBLCHEMBL42336
DrugBankDB00134
ZINCZINC000001532529
PDB chain8pty Chain C Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8pty Cryo-EM structure of human Elp123 in complex with 5'-deoxyadenosine and methionine
Resolution3.58 Å
Binding residue
(original residue number in PDB)		S126 E221 T222 R223 R260
Binding residue
(residue number reindexed from 1)		S42 E137 T138 R139 R176
Annotation score5
Enzymatic activity
Enzyme Commision number 2.3.1.311: tRNA carboxymethyluridine synthase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008607 phosphorylase kinase regulator activity
GO:0016407 acetyltransferase activity
GO:0016746 acyltransferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0106261 tRNA uridine(34) acetyltransferase activity
Biological Process
GO:0001764 neuron migration
GO:0002098 tRNA wobble uridine modification
GO:0002926 tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006417 regulation of translation
GO:0007399 nervous system development
GO:0007417 central nervous system development
GO:0008033 tRNA processing
GO:0030335 positive regulation of cell migration
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0033588 elongator holoenzyme complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8pty, PDBe:8pty, PDBj:8pty
PDBsum8pty
PubMed38750017
UniProtQ9H9T3|ELP3_HUMAN Elongator complex protein 3 (Gene Name=ELP3)

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