Structure of PDB 8avg Chain C Binding Site BS02

Receptor Information
>8avg Chain C (length=435) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGIAVVAVMCKPHRCPHISFTGNICIYCPGGPDSDFEYSTQSYTGYEPTS
MRAIRARYDPFLQTRHRIEQLKQLGHSVDKVEFIVMGGTFMALPEEYRDY
FIRSLHDALSGHTSNNIHEAIKYSERSFTKCVGITIETRPDYCMKRHLSD
MLTYGCTRLEIGVQSVYEDVARDTNRGHTVKAACESFHLAKDSGFKVVTH
MMPDLPNVGLERDIEQFIEFFENPAFRPDGLKLYPTLVIRGTGLYELWKS
GRYRSYSPSDLIELVARILALVPPWTRVYRVQRDIPMPLVSSGVEHGNLR
ELAFARMKDLGIQCRDVRTREVYQVELVRRDYVANGGWETFLSYEDPDQD
ILIGLLRLRKCSEETFRFELGGGVSIVRELHVYGGFGMLLMEEAERIARE
EHGSGKMAVISGVGTRNYYRKIGYRLQGPYMVKML
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain8avg Chain C Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8avg Cryo-EM structure of the fully assembled Elongator complex.
Resolution4.01 Å
Binding residue
(original residue number in PDB)		Y111 Q248 H284 M286 Y318 L321 R367
Binding residue
(residue number reindexed from 1)		Y27 Q164 H200 M202 Y234 L237 R283
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: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:0006357 regulation of transcription by RNA polymerase II
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
View graph for
Cellular Component
External links
PDB RCSB:8avg, PDBe:8avg, PDBj:8avg
PDBsum8avg
PubMed36617428
UniProtQ9CZX0|ELP3_MOUSE Elongator complex protein 3 (Gene Name=Elp3)

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