4Y1L Ligase Nuclear Protein date Feb 08, 2015
title Ubc9 Homodimer The Missing Link In Poly-Sumo Chain Formation
authors Y.A.Aileen, N.D.Ambaye, Y.J.Li, R.Vega, K.Bzymek, J.C.Williams, W.
compound source
Molecule: Sumo-Conjugating Enzyme Ubc9
Chain: A, B
Synonym: Sumo-Protein Ligase,Ubiquitin Carrier Protein 9,Ub Carrier Protein I,Ubiquitin-Conjugating Enzyme E2 I,Ubiquit Ligase I,P18;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2i, Ubc9, Ubce9
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rwd Domain-Containing Protein 3
Chain: C
Synonym: Rwd Domain-Containing Sumoylation Enhancer,Rsume
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rwdd3, Rsume
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.225 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.230 34.860 114.510 90.00 98.53 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand
enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • ubiquitin-protein transferas...
  • SUMO conjugating enzyme acti...


  • C


    Primary referenceRWD Domain as an E2 (Ubc9)-Interaction Module., Alontaga AY, Ambaye ND, Li YJ, Vega R, Chen CH, Bzymek KP, Williams JC, Hu W, Chen Y, J Biol Chem. 2015 Apr 27. pii: jbc.M115.644047. PMID:25918163
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (4y1l.pdb1.gz) 150 Kb
  • CSU: Contacts of Structural Units for 4Y1L
  • Structure Factors (222 Kb)
  • Retrieve 4Y1L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Y1L from S2C, [Save to disk]
  • Re-refined 4y1l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Y1L 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 4Y1L
  • 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 4Y1L, from MSDmotif at EBI
  • Fold representative 4y1l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4y1l] [4y1l_B] [4y1l_C] [4y1l_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4Y1L: [RWD] [UBCc ] by SMART
  • Other resources with information on 4Y1L
  • Community annotation for 4Y1L at PDBWiki (http://pdbwiki.org)

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