5TDC Ligase date Sep 19, 2016
title Crystal Structure Of The Human Ubr-Box Domain From Ubr1 In C With Monomethylated Arginine Peptide.
authors G.Kozlov, J.Munoz-Escobar, E.Matta-Camacho, K.Gehring
compound source
Molecule: E3 Ubiquitin-Protein Ligase Ubr1
Chain: A, C
Synonym: N-Recognin-1,Ubiquitin-Protein Ligase E3-Alpha-1,U Protein Ligase E3-Alpha-I;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubr1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_plasmid: Pgex-6p-1

Molecule: Nmm-Ile-Phe-Ser Peptide
Chain: B, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.149 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.274 49.036 53.634 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.61 Å
ligand NMM, SO4, ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceBound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase., Munoz-Escobar J, Matta-Camacho E, Cho C, Kozlov G, Gehring K, Structure. 2017 Mar 27. pii: S0969-2126(17)30064-3. doi:, 10.1016/j.str.2017.03.004. PMID:28392261
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (5tdc.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (5tdc.pdb2.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 5TDC
  • CSU: Contacts of Structural Units for 5TDC
  • Structure Factors (320 Kb)
  • Retrieve 5TDC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TDC from S2C, [Save to disk]
  • Re-refined 5tdc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TDC 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 5TDC
  • 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 5tdc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tdc_B] [5tdc_D] [5tdc] [5tdc_A] [5tdc_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TDC
  • Community annotation for 5TDC at PDBWiki (http://pdbwiki.org)

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