Structure of PDB 8uq8 Chain A Binding Site BS01

Receptor Information
>8uq8 Chain A (length=426) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GHMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKAS
LCCPFCRRRVSSWTRYHTRRNSLVNVELWTIIQKHYPRECKLRSGSGSAL
KRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLT
IHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVL
LSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAMGSRKES
YSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKR
STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSAKAKTRSSRAGL
QFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDN
KKTRIIPRHLQLAIRNDEELNKLLGR
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 chain8uq8 Chain A Residue 4007 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8uq8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
Resolution2.34 Å
Binding residue
(original residue number in PDB)		C31 H33 C51 C54
Binding residue
(residue number reindexed from 1)		C33 H35 C53 C56
Annotation score4
Enzymatic activity
Enzyme Commision number 2.3.2.23: E2 ubiquitin-conjugating enzyme.
2.3.2.24: (E3-independent) E2 ubiquitin-conjugating enzyme.
2.3.2.27: RING-type E3 ubiquitin transferase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0019787 ubiquitin-like protein transferase activity
GO:0030527 structural constituent of chromatin
GO:0031625 ubiquitin protein ligase binding
GO:0046982 protein heterodimerization activity
GO:0061630 ubiquitin protein ligase activity
GO:0061631 ubiquitin conjugating enzyme activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0000209 protein polyubiquitination
GO:0006281 DNA repair
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006513 protein monoubiquitination
GO:0006915 apoptotic process
GO:0016567 protein ubiquitination
GO:0030514 negative regulation of BMP signaling pathway
GO:0036211 protein modification process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0051865 protein autoubiquitination
GO:0070936 protein K48-linked ubiquitination
GO:0070979 protein K11-linked ubiquitination
GO:0085020 protein K6-linked ubiquitination
GO:1903955 positive regulation of protein targeting to mitochondrion
Cellular Component
GO:0000151 ubiquitin ligase complex
GO:0000786 nucleosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005768 endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8uq8, PDBe:8uq8, PDBj:8uq8
PDBsum8uq8
PubMed38242129
UniProtP04908|H2A1B_HUMAN Histone H2A type 1-B/E (Gene Name=H2AC4);
P61077|UB2D3_HUMAN Ubiquitin-conjugating enzyme E2 D3 (Gene Name=UBE2D3);
Q16778|H2B2E_HUMAN Histone H2B type 2-E (Gene Name=H2BC21);
Q8IYW5|RN168_HUMAN E3 ubiquitin-protein ligase RNF168 (Gene Name=RNF168)

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