4R2Y Ligase date Aug 13, 2014
title Crystal Structure Of Apc11 Ring Domain
authors N.G.Brown, E.R.Watson, F.Weissmann, M.A.Jarvis, R.Vanderlinden, C.R.R.Grace, J.J.Frye, P.Dube, R.Qiao, G.Petzold, S.E.Cho, O.Alsh J.Bao, J.Zheng, A.Nourse, I.Kurinov, J.M.Peters, H.Stark, B.A.Sch
compound source
Molecule: Anaphase-Promoting Complex Subunit 11
Chain: A, B, C, D
Fragment: Ring Domain (Unp Residues 17-84)
Synonym: Apc11, Cyclosome Subunit 11, Hepatocellular Carcin Associated Ring Finger Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc11, Hspc214
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 2 1
R_factor 0.192 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
52.446 39.876 65.038 90.00 108.49 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand ZN enzyme
A, D, C, B

Primary referenceMechanism of Polyubiquitination by Human Anaphase-Promoting Complex: RING Repurposing for Ubiquitin Chain Assembly., Brown NG, Watson ER, Weissmann F, Jarvis MA, VanderLinden R, Grace CR, Frye JJ, Qiao R, Dube P, Petzold G, Cho SE, Alsharif O, Bao J, Davidson IF, Zheng JJ, Nourse A, Kurinov I, Peters JM, Stark H, Schulman BA, Mol Cell. 2014 Oct 8. pii: S1097-2765(14)00716-3. doi:, 10.1016/j.molcel.2014.09.009. PMID:25306923
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (4r2y.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (4r2y.pdb2.gz) 24 Kb
  • Biological Unit Coordinates (4r2y.pdb3.gz) 25 Kb
  • Biological Unit Coordinates (4r2y.pdb4.gz) 24 Kb
  • Biological Unit Coordinates (4r2y.pdb5.gz) 92 Kb
  • Biological Unit Coordinates (4r2y.pdb6.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 4R2Y
  • CSU: Contacts of Structural Units for 4R2Y
  • Structure Factors (431 Kb)
  • Retrieve 4R2Y in mmCIF format [Save to disk]
  • Re-refined 4r2y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R2Y 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 4R2Y
  • 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 4R2Y, from MSDmotif at EBI
  • Fold representative 4r2y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r2y_C] [4r2y] [4r2y_B] [4r2y_D] [4r2y_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4R2Y: [RING ] by SMART
  • Other resources with information on 4R2Y
  • Community annotation for 4R2Y at PDBWiki (http://pdbwiki.org)

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