Structure of PDB 8ptz Chain C Binding Site BS03

Receptor Information
>8ptz Chain C (length=538) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPAELMMLTIGDVIKQLIEAHEQGKDIDLNKVKTKTAAKYGLSAQPRLVD
IIAAVPPQYRKVLMPKLKAKPIRTASGIAVVAVMCKPHRCPHISFTGNIC
VYCPGGPDSDFEYSTQSYTGYEPTSMRAIRARYDPFLQTRHRIEQLKQLG
HSVDKVEFIVMGGTFMALPEEYRDYFIRNLHDALSGHTSNNIYEAVKYSE
RSLTKCIGITIETRPDYCMKRHLSDMLTYGCTRLEIGVQSVYEDVARDTN
RGHTVKAVCESFHLAKDSGFKVVAHMMPDLPNVGLERDIEQFTEFFENPA
FRPDGLKLYPTLVIRGTGLYELWKSGRYKSYSPSDLVELVARILALVPPW
TRVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGIQCRDVRTREVGIQ
EIHHKVRPYQVELVRRDYVANGGWETFLSYEDPDQDILIGLLRLRKCSEE
TFRFELGGGVSIVRELHVYGSVVPVSSRDPTKFQHQGFGMLLMEEAERIA
REEHGSGKIAVISGVGTRNYYRKIGYRLQGPYMVKMLK
Ligand information
Ligand IDA2U
InChIInChI=1S/C23H40N7O16P3S/c1-4-50-8-7-25-14(31)5-6-26-21(34)18(33)23(2,3)10-43-49(40,41)46-48(38,39)42-9-13-17(45-47(35,36)37)16(32)22(44-13)30-12-29-15-19(24)27-11-28-20(15)30/h11-13,16-18,22,32-33H,4-10H2,1-3H3,(H,25,31)(H,26,34)(H,38,39)(H,40,41)(H2,24,27,28)(H2,35,36,37)/t13-,16-,17-,18+,22+/m1/s1
InChIKeyYGTAAWZKDDQUQN-RJFKWGFDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCSCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
CACTVS 3.385CCSCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
CACTVS 3.385CCSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.7CCSCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
FormulaC23 H40 N7 O16 P3 S
NameS-Ethyl-CoA
ChEMBL
DrugBank
ZINC
PDB chain8ptz Chain C Residue 603 [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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PDB8ptz Cryo-EM structure of human Elp123 in complex with tRNA, S-ethyl-CoA, 5'-deoxyadenosine and methionine
Resolution3.35 Å
Binding residue
(original residue number in PDB)		K164 K214 I216 L475 H476 V477 R487 Q493 H494 G496 M499 G525 T526 Y529 Y530
Binding residue
(residue number reindexed from 1)		K155 K205 I207 L466 H467 V468 R478 Q484 H485 G487 M490 G516 T517 Y520 Y521
Annotation score3
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:8ptz, PDBe:8ptz, PDBj:8ptz
PDBsum8ptz
PubMed38750017
UniProtQ9H9T3|ELP3_HUMAN Elongator complex protein 3 (Gene Name=ELP3)

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