Structure of PDB 5d1k Chain A

Receptor sequence

>5d1kA (length=146) Species: 9606 (Homo sapiens)

ALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFF
LTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISK
VLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

3D structure

• PDB: 5d1k Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B.
• Chain: A
• Resolution: 1.78 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C85
• Catalytic site (residue number reindexed from 1): C84
• 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	OXL	A	W141 Y145	W140 Y144

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:5d1k, PDBe:5d1k, PDBj:5d1k
• PDBsum: 5d1k
• PubMed: 26475854
• UniProt: P62837|UB2D2_HUMAN Ubiquitin-conjugating enzyme E2 D2 (Gene Name=UBE2D2)