1Y8R Ligase date Dec 13, 2004
title Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
authors L.M.Lois, C.D.Lima
compound source
Molecule: Ubiquitin-Like 1 Activating Enzyme E1a
Chain: A, D
Synonym: Sumo-1 Activating Enzyme Subunit 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Uble1a, Sae1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21de3cp
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11c

Molecule: Ubiquitin-Like 2 Activating Enzyme E1b
Chain: B, E
Synonym: Sumo-1 Activating Enzyme Subunit 2; Anthracycline- Associated Resistance Arx; Hrihfb2115;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Uble1b, Sae2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21de3cp
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ubiquitin-Like Protein Smt3c
Chain: C, F
Synonym: Ubiquitin-Homology Domain Protein Pic1; Ubiquitin- Like Protein Ubl1; Ubiquitin-Related Protein Sumo-1; Gap Modifying Protein 1; Gmp1; Sentrin; Oksw-Cl.43;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubl1, Sumo-1, Smt3c, Smt3h3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 21 21 2
R_factor 0.220 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
117.197 215.151 100.870 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand ATP, MG, ZN enzyme
related structures by homologous chain: 1TGZ, 1Y8Q, 2BF8
Gene
Ontology
ChainFunctionProcessComponent
A, D
  • ubiquitin activating enzyme ...
  • enzyme activator activity


  • E, B


    F, C


    Primary referenceStructures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1., Lois LM, Lima CD, EMBO J 2005 Jan 20;. PMID:15660128
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (307 Kb) [Save to disk]
  • Biological Unit Coordinates (1y8r.pdb1.gz) 151 Kb
  • Biological Unit Coordinates (1y8r.pdb2.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 1Y8R
  • CSU: Contacts of Structural Units for 1Y8R
  • Likely Quarternary Molecular Structure file(s) for 1Y8R
  • Structure Factors (558 Kb)
  • Retrieve 1Y8R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y8R from S2C, [Save to disk]
  • Re-refined 1y8r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y8R in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1Y8R
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1Y8R, from MSDmotif at EBI
  • Fold representative 1y8r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y8r] [1y8r_C] [1y8r_E] [1y8r_D] [1y8r_F] [1y8r_A] [1y8r_B]
  • SWISS-PROT database: [Q9UBE0] [Q9UBT2] [P63165]
  • Domain organization of [SAE1_HUMAN] [SAE2_HUMAN] [SUMO1_HUMAN] by SWISSPFAM
  • Domain found in 1Y8R: [UBQ ] by SMART
  • Other resources with information on 1Y8R
  • Community annotation for 1Y8R at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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