1YX5 Hydrolase date Feb 19, 2005
title Solution Structure Of S5a Uim-1ubiquitin Complex
authors Q.Wang, P.Young, K.J.Walters
compound source
Molecule: 26s Proteasome Non-Atpase Regulatory Subunit 4
Chain: A
Fragment: Polyubiquitin Binding Region Of S5a
Synonym: 26s Proteasome Regulatory Subunit S5a, Rpn10, Multiubiquitin Chain Binding Protein, Antisecretory Factor- 1, Af, Asf;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Psmd4, Mcb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin
Chain: B
Fragment: Sequence Database Residues 1-76
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
methodSolution NMR
related structures by homologous chain: 1YX4, 1YX6
Primary referenceStructure of s5a bound to monoubiquitin provides a model for polyubiquitin recognition., Wang Q, Young P, Walters KJ, J Mol Biol 2005 May 6;348(3):727-39. PMID:15826667
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (870 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1YX5
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1YX5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YX5 from S2C, [Save to disk]
  • View 1YX5 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 1YX5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YX5, from MSDmotif at EBI
  • Fold representative 1yx5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yx5] [1yx5_B] [1yx5_A]
  • SWISS-PROT database: [P55036] [P62988]
  • Domain organization of [PSMD4_HUMAN] [UBIQ_HUMAN] by SWISSPFAM
  • Domains found in 1YX5: [UBQ] [UIM ] by SMART
  • Other resources with information on 1YX5
  • Community annotation for 1YX5 at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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