3cmm Summary

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Crystal Structure of the Uba1-Ubiquitin Complex

The structure was published by Lee, I. and Schindelin, H., in 2008 in a paper entitled "Structural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.7 Å and deposited in 2008.

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

This PDB entry contains a complex of 2 biomacromolecules, namely Ubiquitin-activating enzyme E1 1 and Ubiquitin.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

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 Ubiquitin-activating enzyme E1 1 P22515 (10-1024) (UBA1_YEAST)search Saccharomyces cerevisiae S288csearch 99% 1015 99%
C Ubiquitin-activating enzyme E1 1 P22515 (10-1024) (UBA1_YEAST)search Saccharomyces cerevisiae S288csearch 99% 1015 99%
B Ubiquitin P0CG63 (305-380) (UBI4P_YEAST)search Saccharomyces cerevisiae S288csearch < 90% 76 100%
D Ubiquitin P0CG63 (305-380) (UBI4P_YEAST)search Saccharomyces cerevisiae S288csearch < 90% 76 100%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P22515 (10 - 1024) Ubiquitin-activating enzyme E1 1 Saccharomyces cerevisiae
P0CG63 (305 - 380) Ubiquitin Saccharomyces cerevisiae

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, C (P22515) PF00899: ThiF familysearch, PF02134: Repeat in ubiquitin-activating (UBA) proteinsearch, PF09358: Ubiquitin-activating enzyme e1 C-terminal domainsearch, PF10585: Ubiquitin-activating enzyme active sitesearch
B, D Ubiquitin-relatedsearch Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1search Ubiquitin familysearch

Chain ID Molecular function (GO) Cellular component (GO) Biological process (GO)
A, C (P22515) ligase activitysearch ubiquitin activating enzyme activitysearch ATP bindingsearch catalytic activitysearch nucleotide bindingsearch small protein activating enzyme activitysearch nucleussearch cytoplasmsearch cellular protein modification processsearch protein ubiquitinationsearch

Chain InterPro annotation
A, C Ubiquitin/SUMO-activating enzyme E1search Ubiquitin-activating enzyme repeatsearch UBA/THIF-type NAD/FAD binding foldsearch Molybdenum cofactor biosynthesis, MoeBsearch NAD(P)-binding domainsearch Ubiquitin-activating enzyme, E1, active sitesearch Ubiquitin-activating enzyme, E1search Ubiquitin-activating enzyme e1, C-terminalsearch Ubiquitin-activating enzymesearch Ubiquitin-like 1 activating enzyme, catalytic cysteine domainsearch
B, D Ubiquitin-likesearch Ubiquitin conserved sitesearch Ubiquitinsearch Ubiquitin-related domainsearch