5EHD Oxidoreductase date Oct 28, 2015
title Crystal Structure Of Human Nucleophosmin-Core In Complex Wit Cytochrome C
authors N.Bernardo-Garcia, J.A.Hermoso, K.Gonzalez-Arzola, I.Diaz-Moren La Rosa
compound source
Molecule: Nucleophosmin
Chain: A, B, C, D, E, F, G, H, I, J, a, b, c, d, e, f, g, h
Synonym: Npm,Nucleolar Phosphoprotein B23,Nucleolar Protein Numatrin;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Npm1, Npm
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: P 1 21 1
R_factor 0.164 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
58.799 179.720 104.300 90.00 94.32 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand CL enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (726 Kb) [Save to disk]
  • Biological Unit Coordinates (5ehd.pdb1.gz) 176 Kb
  • Biological Unit Coordinates (5ehd.pdb2.gz) 179 Kb
  • Biological Unit Coordinates (5ehd.pdb3.gz) 177 Kb
  • Biological Unit Coordinates (5ehd.pdb4.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 5EHD
  • CSU: Contacts of Structural Units for 5EHD
  • Structure Factors (4828 Kb)
  • Retrieve 5EHD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EHD from S2C, [Save to disk]
  • Re-refined 5ehd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EHD 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 5EHD
  • 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 5ehd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ehd_i] [5ehd_g] [5ehd_e] [5ehd_c] [5ehd_I] [5ehd_a] [5ehd_J] [5ehd_b] [5ehd] [5ehd_E] [5ehd_f] [5ehd_j] [5ehd_B] [5ehd_h] [5ehd_d] [5ehd_D] [5ehd_F] [5ehd_A] [5ehd_H] [5ehd_C] [5ehd_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EHD
  • Community annotation for 5EHD at PDBWiki (http://pdbwiki.org)

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