1X23 Ligase date Apr 19, 2005
title Crystal Structure Of Ubch5c
authors M.Nakanishi, N.Teshima, T.Mizushima, S.Murata, K.Tanaka, T.Yamane
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 D3
Chain: A, B, C, D
Synonym: Ubiquitin-Protein Ligase D3, Ubiquitin Carrier Pro Ubiquitin-Conjugating Enzyme E2-17 Kda 3, E217, Kb 3;
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p-1
symmetry Space Group: P 1 21 1
R_factor 0.199 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.998 44.334 97.584 90.00 93.36 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
related structures by homologous chain: 1QCQ, 1Y6L
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (1x23.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (1x23.pdb2.gz) 29 Kb
  • Biological Unit Coordinates (1x23.pdb3.gz) 28 Kb
  • Biological Unit Coordinates (1x23.pdb4.gz) 28 Kb
  • CSU: Contacts of Structural Units for 1X23
  • Likely Quarternary Molecular Structure file(s) for 1X23
  • Structure Factors (327 Kb)
  • Retrieve 1X23 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1X23 from S2C, [Save to disk]
  • Re-refined 1x23 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1X23 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 1X23
  • 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
  • 3D motif for 1X23, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1x23_B] [1x23_A] [1x23] [1x23_C] [1x23_D]
  • SWISS-PROT database: [P61077]
  • Domain organization of [UB2D3_HUMAN] by SWISSPFAM
  • Domain found in 1X23: [UBCc ] by SMART
  • Other resources with information on 1X23
  • Community annotation for 1X23 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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