Structure of PDB 6yub Chain A Binding Site BS01

Receptor Information
>6yub Chain A (length=423) Species: 209285 (Thermochaetoides thermophila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STQKSLSKEEIERYSRQMIVPGMGKEGQLRLMNAKVLIIGAGGLGCPAAQ
YLAGAGVGTIGIVDGDSVETSNLHRQVAHATKRVGMLKVDSLITHLIEIN
PLPVYVPYRFDLTPQNAAQIIKPWDVILDCTDNPATRYLISDVCVLLGKP
LVSAASVQKSGQLIVLNCPPTPQGVVNKKAAPCYRCCFKKPGIMGPVVGM
MGVAQAGEAIKILVSQLHMPPKEGEEVSPEKNLVQPTLLIYTYDLNSAIG
PYSFRALKMGGRKKDCFACGENSTLTLDGIKSGNPNYVGNMTQSTNLAPE
DRITATAYNEKRRNGELGEHILLDTREKEHFSFGSIPGAVNVPFSKFLVK
ASSIKRPAELLPMQPASDEAPIVVVCRRGQDSQEVVEKLKELGLDNGGKR
KIMDIVGGMKAWRDEVDPDFPFI
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain6yub Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6yub Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation.
Resolution2.195 Å
Binding residue
(original residue number in PDB)		C185 C188 C280 C283
Binding residue
(residue number reindexed from 1)		C183 C186 C266 C269
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.80: molybdopterin-synthase adenylyltransferase.
2.8.1.11: molybdopterin synthase sulfurtransferase.
Gene Ontology
Molecular Function
GO:0004792 thiosulfate sulfurtransferase activity
GO:0005524 ATP binding
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0016783 sulfurtransferase activity
GO:0042292 URM1 activating enzyme activity
GO:0046872 metal ion binding
GO:0061604 molybdopterin-synthase sulfurtransferase activity
GO:0061605 molybdopterin-synthase adenylyltransferase activity
GO:0070566 adenylyltransferase activity
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0002143 tRNA wobble position uridine thiolation
GO:0006777 Mo-molybdopterin cofactor biosynthetic process
GO:0008033 tRNA processing
GO:0032447 protein urmylation
GO:0034227 tRNA thio-modification
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6yub, PDBe:6yub, PDBj:6yub
PDBsum6yub
PubMed32901956
UniProtG0SC54

[Back to BioLiP]