5DKA Ligase date Sep 03, 2015
title A C2hc Zinc Finger Is Essential For The Activity Of The Ring Ligase Rnf125
authors D.R.Boer, M.Coll, M.J.Bijlmakers
compound source
Molecule: E3 Ubiquitin-Protein Ligase Rnf125
Chain: A, B
Synonym: Ring Finger Protein 125,T-Cell Ring Activation Pro Trac-1;
Ec: 6.3.2.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnf125
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
symmetry Space Group: P 21 21 21
R_factor 0.210 R_Free 0.239
length a length b length c angle alpha angle beta angle gamma
51.670 52.320 73.970 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand CL, MG, ZN enzyme Ligase E.C.6.3.2 BRENDA
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (5dka.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (5dka.pdb2.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 5DKA
  • CSU: Contacts of Structural Units for 5DKA
  • Structure Factors (499 Kb)
  • Retrieve 5DKA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DKA from S2C, [Save to disk]
  • Re-refined 5dka structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DKA 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 5DKA
  • 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
  • Fold representative 5dka from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dka_A] [5dka] [5dka_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DKA: [FN2] [RING] [ZnF_C2H2 ] by SMART
  • Other resources with information on 5DKA
  • Community annotation for 5DKA at PDBWiki (http://pdbwiki.org)

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