1Y6L Ligase date Dec 06, 2004
title Human Ubiquitin Conjugating Enzyme E2e2
authors J.R.Walker, G.V.Avvakumov, E.M.Newman, F.Mackenzie, I.Kozieradzk A.Bochkarev, M.Sundstrom, C.Arrowsmith, A.Edwards, S.Dhe-Pagano Structural Genomics Consortium (Sgc)
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2e2
Chain: A, B, C
Fragment: Residues 55-201
Synonym: Ubiquitin-Protein Ligase E2, Ubiquitin Carrier Pro Ubch8;
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2e2, Ubch8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.192 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.109 36.110 130.568 90.00 99.92 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
related structures by homologous chain: 1X23, 1Z2U
Primary referenceA human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen., Sheng Y, Hong JH, Doherty R, Srikumar T, Shloush J, Avvakumov GV, Walker JR, Xue S, Neculai D, Wan JW, Kim SK, Arrowsmith CH, Raught B, Dhe-Paganon S, Mol Cell Proteomics. 2012 Aug;11(8):329-41. Epub 2012 Apr 10. PMID:22496338
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (1y6l.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (1y6l.pdb2.gz) 27 Kb
  • Biological Unit Coordinates (1y6l.pdb3.gz) 27 Kb
  • CSU: Contacts of Structural Units for 1Y6L
  • Likely Quarternary Molecular Structure file(s) for 1Y6L
  • Structure Factors (633 Kb)
  • Retrieve 1Y6L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y6L from S2C, [Save to disk]
  • Re-refined 1y6l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y6L 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 1Y6L
  • 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 1Y6L, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1y6la_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1y6lb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1y6lc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1y6l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y6l_A] [1y6l_B] [1y6l_C] [1y6l]
  • SWISS-PROT database: [Q96LR5]
  • Domain organization of [UB2E2_HUMAN] by SWISSPFAM
  • Domain found in 1Y6L: [UBCc ] by SMART
  • Other resources with information on 1Y6L
  • Community annotation for 1Y6L 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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