Structure of PDB 8agv Chain e Binding Site BS03

Receptor Information
>8agv Chain e (length=1527) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFGGINTFQQYNTDLGLGHNGVRISLNYFDGLPDPSLLNSLYSNELKLIF
KSLLKRDETTKEKALMDLSNLISDFNQNEYFFNDIFLLCWSQIYAKLIIS
DYKVIRLQSHQITIMLVKSLRKKISKFLKDFIPLILLGTCELDYSVSKPS
LNELTECFNKDPAKINALWAVFQEQLLNLVKEIVVNENEDTISDERYSSK
EESEFRYHRVIASAVLLLIKLFVHNKDVSERNSSSLKVILSDESIWKLLN
LKNGQNTNAYETVLRLIDVLYTRGYMPSHKNIMKLAVKKLLKSLTHITSK
NILKVCPVLPSILNLLATLDDYEDGTIWSYDKSSKEKVLKFLSVSRTSPS
PGFFNAVFALYSSTKRHSFLDYYLEWLPFWQKSVQRLNEKGFSARNSAEV
LNEFWTNFLKFAEDSSEERVKKMVESEIFNSLSCGKSLSEYTKLNQTLSG
VFPPDKWEREIEDYFTSDEDIRKIKVSFEKNLFALLVTSPNNESAISRLF
DFFVQLIETDPSNVFNKYDGVYDALNYFLDSDMIFLNGKIGKFINEIPTL
VQESTYQNFAGIMAQYSNSKFFKMNTDAITSLEDFFIVALSFNLPKTIIL
ATMNELDNDIYQQLMKSDSLELELYIEDFMKNYKFDDSGEIFKGNNKFLN
QRTITTLYRSAVANGQVEQFCAVLSKLDETFFSTLLLNTDFLSCALYEVS
EDTNEKLFKLSLQLAKGNSEIANKLAQVILQHAQVYFSPGAKEKYVTHAV
ELINGCNDTSQIFFPANAIEVFARYMPAIDYRSSLVSSLSTNTHLLLTDD
KPINLKNMQKLIRYALFLDALLDALPERVNNHIVAFITVVSELVTDYNCL
SEEPNDLYYDFGHTFFKHGKVNLNFSDIVGNVIQPANGGDAMLTFDIAES
NSVYFFYYSRVLYKVLLNSIDTVSSTTLNGLLASVESFVTKTVRDQKSTD
KDYLLCAILLLMFNRSNSKDEITKLRTLLASQLIGIREVELVDQEFKSLA
LLNNLLDIPQADKQFVPIAPQRLNMIFRSILKWLDSDLAYEPSFSTVRLL
LLDFFTKLMRFEGVRDMGITAFELSERLLADSLSMCQIDDTLYLLELRSS
CLNLYETLSQEYGDEIQENLIELMFLNFNQERNNQVSTLFYQKLYKVISS
MELKKLESQYKRIFEVVLNDKDIGSNINQSRLLTTLLGSLVVKTQQDIII
EYELRINSKFKLPQKLLQKVTDEVPKEYLEYENKNSFIKYLWYWHLILMY
FKDTSYNMRQIFIEQLKEAGLINRMFDFITDQIDLRDTEFWKQVDTKEIS
EYNIVGNNFSPYKEDIFEECKKLLGHTLYQLFNNVGCLTSIWWLNIKDRT
LQNDIEKFVSEFISPILIKNEFDDINSKMDRLTALTIKLNNITNEVKASY
LIDDQKLEISFKLPKNYPLTNIQVNGVSRVGISEQKWKQWIMSTQHVITG
MNGSVLDSLELFTKNVHLQFSGFEECAICYSILHAVDRKLPSKTCPTCKN
KFHGACLYKWFRSSGNNTCPLCRSEIP
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 chain8agv Chain e Residue 2002 [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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PDB8agv Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		C1508 C1511 H1535 C1538
Binding residue
(residue number reindexed from 1)		C1476 C1479 H1503 C1506
Annotation score4
Enzymatic activity
Enzyme Commision number 2.3.2.27: RING-type E3 ubiquitin transferase.
Gene Ontology
Molecular Function
GO:0004842 ubiquitin-protein transferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0043023 ribosomal large subunit binding
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity
Biological Process
GO:0006325 chromatin organization
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0010498 proteasomal protein catabolic process
GO:0016567 protein ubiquitination
GO:0030163 protein catabolic process
GO:0031509 subtelomeric heterochromatin formation
GO:0072344 rescue of stalled ribosome
GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0022626 cytosolic ribosome
GO:1990112 RQC complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8agv, PDBe:8agv, PDBj:8agv
PDBsum8agv
PubMed36804914
UniProtQ04781|LTN1_YEAST E3 ubiquitin-protein ligase listerin (Gene Name=RKR1)

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