5AZW Protein Transport date Oct 23, 2015
title Crystal Structure Of P24beta1 Gold Domain
authors M.Nagae, Y.Yamaguchi
compound source
Molecule: Transmembrane Emp24 Domain-Containing Protein 2
Chain: A, B
Synonym: Membrane Protein P24a,P24,P24 Family Protein Beta- P24beta1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tmed2, Rnp24
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.221 R_Free 0.233
length a length b length c angle alpha angle beta angle gamma
97.772 35.664 62.312 90.00 129.22 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand EDO enzyme
Primary reference3D Structure and Interaction of p24beta and p24delta Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport., Nagae M, Hirata T, Morita-Matsumoto K, Theiler R, Fujita M, Kinoshita T, Yamaguchi Y, J Mol Biol. 2016 Aug 25. pii: S0022-2836(16)30342-4. doi:, 10.1016/j.jmb.2016.08.023. PMID:27569046
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (5azw.pdb1.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 5AZW
  • CSU: Contacts of Structural Units for 5AZW
  • Structure Factors (528 Kb)
  • Retrieve 5AZW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5AZW from S2C, [Save to disk]
  • Re-refined 5azw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5AZW 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 5AZW
  • 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 5azw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5azw_B] [5azw] [5azw_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5AZW: [EMP24_GP25L ] by SMART
  • Other resources with information on 5AZW
  • Community annotation for 5AZW at PDBWiki (http://pdbwiki.org)

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