Structure of PDB 8sn3 Chain L

Receptor sequence
>8sn3L (length=148) Species: 9606 (Homo sapiens) [Search protein sequence]
HMALKRINKELSDLARDPPAQISAGPVGDDMFHWQATIMGPNDSPYQGGV
FFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTI
SKVLLSIASLLDDPNPDDPKVPEIARIYKTDRDKYNRISREWTQKYAM
3D structure
PDB8sn3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1)
ChainL
Resolution3.8 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.3.2.23: E2 ubiquitin-conjugating enzyme.
2.3.2.24: (E3-independent) E2 ubiquitin-conjugating enzyme.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna L P121 R125 P122 R126
Gene Ontology
Molecular Function
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:0031625 ubiquitin protein ligase binding
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: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:8sn3, PDBe:8sn3, PDBj:8sn3
PDBsum8sn3
PubMed38242129
UniProtP61077|UB2D3_HUMAN Ubiquitin-conjugating enzyme E2 D3 (Gene Name=UBE2D3)

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