Structure of PDB 8d4x Chain A Binding Site BS03

Receptor Information
>8d4x Chain A (length=1684) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTSIHFVVHPLPGTEDQLNDRLREVSEKLNKYNLNSHPPLNVLEQATIKQ
CVVGPNHAAFLLEDGRVCRIGFSVQPDRLSPVSLGEDLQWWPDKDGTKFI
CIGALYSELLAVSSKGELYQWKWSESEPYRNAQNPSLHHPRATFLGLTNE
KIVLLSANSIRATVATENNKVATWVDETLSSVASKLEHTAQTYSELQGER
IVSLHCCALYTCAQLENSLYWWGVVPFSQRKKMLEKARAKNKPLYHAGAV
AFSISAGIPKVGVLMESVWNMNDSCRFQLRSPESLKNEEQWSLREVVFVE
DVVPDCFQRTPKKLCIPEKTEILAVNVDSKGVHAVLKTGNWVRYCIFDLA
TGKAEQENNFPTSSIAFLGQNERNVAIFTAGQESPIILRDGNGTIYPMAK
DCMGGIRDPDWLDLPPISSLGMGVHSLINLPANSTIKKKAAVIIMAVEKQ
TLMQHILRCDYEACRQYLMNLEQAVVLEQNLQMLQTFISHRCDGNRNILH
ACVSVCFPTSNKVESKDRKANAHFILKLLCDSVVLQPYLRELLSAKDARG
MTPFMSAVSGRAYPAAITILETAQKIAKAEISSSEKEEDVFMGMVCPSGT
NPDDSPLYVLCCNDTCSFTWTGAEHINQDIFECRTCGLLESLCCCTECAR
VCHKGHDCKLKRTSPTAYCDCWEKCKCKTLIAGQKSARLDLLYRLLTATN
LVTLPNSRGEHLLLFLVQTVARQTVEHCQYRPPRIREDSDMPDHDLEPPR
FAQLALERVLQDWNALKSMIMFGSQENKDPLSASSRIGHLLPEEQVYLNQ
QSGTIRLDCFTHCLIVKCTADILLLDTLLGTLVKELQNKYTPGRREEAIA
VTMRFLRSVARVFVILSVEMASSKKKNNFIPQPIGKCKRVFQALLPYAVE
ELCNVAESLIVPVRMGIARPTAPFTLASTSIDAMQGSEELFSVEPLPPRP
SSMLDEPLERTTNSSHANGAAQAPRSMQWAVRNNASSYLTSASSLARAYS
IVIRQISDLMGLIPKYNHLVYSQIPAAVKLTYQDAVNLQNYVEEKLIPTW
NWMVSIMDSTEAQLRYGSALASAGDPGHPNHPLHASQNSARRMSARGDFL
NYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIYWIKAMNQQTTGQ
NHPFFRRSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNARKEDLFG
RPSQGLYSSSASSGKCLMEVTVDRNCLEVLPTKMSPPLTSFRPQCSFMGM
VISHDMLLGRWRLSLELFGRVFMEDVGAEPGSILTELGGFEVKESKFRRE
MEKLRNQQSRDLSLEVDRDRDLLIQQTMRQLNNHFGRRCATTPMAVHRVK
VTFKDEPGEGSGVARSFYTAIAQAFLSNEKLPNLECIQNDNAPLFYQPGK
RGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITLNRHVIKVLLG
RKVNWHDFAFFDPVMYESLRQLILASQSSDADAVFSAMDLAFAIDLCKEE
GGGQVELIPNGVNIPVTPQNVYEYVRKYAEHRMLVVAEQPLHAMRKGLLD
VLPKNSLEDLTAEDFRLLVNGCGEVNVQMLISFTSFNDESGENAEKLLQF
KRWFWSIVEKMSMTERQDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQ
HLPTANTCISRLYVPLYSSKQILKQKLLLAIKTK
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 chain8d4x Chain A Residue 2803 [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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PDB8d4x Structure of the human UBR5 E3 ubiquitin ligase.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		C1199 H1216 H1219
Binding residue
(residue number reindexed from 1)		C636 H653 H656
Annotation score4
Enzymatic activity
Enzyme Commision number 2.3.2.26: HECT-type E3 ubiquitin transferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0034450 ubiquitin-ubiquitin ligase activity
GO:0043130 ubiquitin binding
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity
Biological Process
GO:0000209 protein polyubiquitination
GO:0006281 DNA repair
GO:0006974 DNA damage response
GO:0010628 positive regulation of gene expression
GO:0016567 protein ubiquitination
GO:0033696 heterochromatin boundary formation
GO:0035519 protein K29-linked ubiquitination
GO:0042307 positive regulation of protein import into nucleus
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045879 negative regulation of smoothened signaling pathway
GO:0050847 progesterone receptor signaling pathway
GO:0070936 protein K48-linked ubiquitination
GO:0070979 protein K11-linked ubiquitination
GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system
GO:0071630 nuclear protein quality control by the ubiquitin-proteasome system
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:0140455 cytoplasm protein quality control
GO:0140861 DNA repair-dependent chromatin remodeling
GO:0141198 protein branched polyubiquitination
Cellular Component
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0032991 protein-containing complex
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8d4x, PDBe:8d4x, PDBj:8d4x
PDBsum8d4x
PubMed37040767
UniProtO95071|UBR5_HUMAN E3 ubiquitin-protein ligase UBR5 (Gene Name=UBR5)

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