Structure of PDB 6ttu Chain D

Receptor sequence

>6ttuD (length=146) Species: 9606 (Homo sapiens)

ALKRIHKELNDLARDPPAQISAGPVGDDMFHWQATIMGPNDSPYQGGVFF
LTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISK
VLLSIASLLDDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

3D structure

• PDB: 6ttu NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly.
• Chain: D
• Resolution: 3.7 Å

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	peptide	D	C85 D117 P118	C84 D116 P117

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:0000209 protein polyubiquitination
• GO:0006511 ubiquitin-dependent protein catabolic process
• GO:0016567 protein ubiquitination
• GO:0036211 protein modification process
• GO:0051865 protein autoubiquitination
• GO:0070936 protein K48-linked ubiquitination

Cellular Component

• GO:0000151 ubiquitin ligase complex
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005829 cytosol
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:6ttu, PDBe:6ttu, PDBj:6ttu
• PDBsum: 6ttu
• PubMed: 32051583
• UniProt: P62837|UB2D2_HUMAN Ubiquitin-conjugating enzyme E2 D2 (Gene Name=UBE2D2)