Structure of PDB 8sn3 Chain L Binding Site BS01

Receptor Information
>8sn3 Chain L (length=148) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMALKRINKELSDLARDPPAQISAGPVGDDMFHWQATIMGPNDSPYQGGV
FFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTI
SKVLLSIASLLDDPNPDDPKVPEIARIYKTDRDKYNRISREWTQKYAM
Ligand information
>8sn3 Chain J (length=147) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
atcggatgtatatatctgacacgtgcctggagactagggagtaatcccct
tggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgcta
gagctgtctacgaccaattgagcggcctcggcaccgggattctcgat
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]
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)
Resolution3.8 Å
Binding residue
(original residue number in PDB)		P121 R125
Binding residue
(residue number reindexed from 1)		P122 R126
Enzymatic activity
Enzyme Commision number 2.3.2.23: E2 ubiquitin-conjugating enzyme.
2.3.2.24: (E3-independent) E2 ubiquitin-conjugating enzyme.
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8sn3, PDBe:8sn3, PDBj:8sn3
PDBsum8sn3
PubMed38242129
UniProtP61077|UB2D3_HUMAN Ubiquitin-conjugating enzyme E2 D3 (Gene Name=UBE2D3)

[Back to BioLiP]