2bkr Summary

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NEDD8 NEDP1 COMPLEX

The structure was published by Shen, L.N., Liu, H., Dong, C., Xirodimas, D., Naismith, J.H., and Hay, R.T., in 2005 in a paper entitled "Structural Basis of Nedd8 Ubiquitin Discrimination by the Deneddylating Enzyme Nedp1" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.9 Å and deposited in 2005.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 2 biomacromolecules, namely SENTRIN-SPECIFIC PROTEASE 8 and NEDDYLIN.

The molecule most likely forms heterodimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A SENTRIN-SPECIFIC PROTEASE 8 Q96LD8 (1-212) (SENP8_HUMAN)search Homo sapienssearch 100% 212 100%
B NEDDYLIN Q15843 (1-76) (NEDD8_HUMAN)search Homo sapienssearch 94% 77 100%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
Q96LD8 (1 - 212) SENTRIN-SPECIFIC PROTEASE 8 Homo sapiens
Q15843 (1 - 76) NEDDYLIN Homo sapiens

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A (Q96LD8) Adenain-likesearch PF02902: Ulp1 protease family, C-terminal catalytic domainsearch
B (Q15843) Ubiquitin-relatedsearch Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1search PF00240: Ubiquitin familysearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A (Q96LD8) hydrolase activitysearch cysteine-type peptidase activitysearch peptidase activitysearch proteolysissearch
B (Q15843) protein bindingsearch ubiquitin protein ligase bindingsearch proteolysissearch ubiquitin-dependent protein catabolic processsearch protein localizationsearch protein neddylationsearch cellular protein modification processsearch transforming growth factor beta receptor signaling pathwaysearch anatomical structure morphogenesissearch response to organic cyclic compoundsearch regulation of transcription from RNA polymerase II promotersearch nucleussearch extracellular vesicular exosomesearch cytosolsearch

Chain InterPro annotation
A Peptidase C48, SUMO/Sentrin/Ubl1search
B Ubiquitin-likesearch Ubiquitin conserved sitesearch Ubiquitinsearch Ubiquitin-related domainsearch