5YD6 Transcription date Sep 11, 2017
title Crystal Structure Of Pg-Bound Nurr1-Lbd
authors R.Sreekanth, H.S.Yoon
compound source
Molecule: Nuclear Receptor Subfamily 4 Group A Member 2
Chain: A, B, C, D
Fragment: Unp Residues 328-598
Synonym: Immediate-Early Response Protein Not,Orphan Nuclea Nurr1,Transcriptionally-Inducible Nuclear Receptor;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr4a2, Not, Nurr1, Tinur
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet-Sumo
symmetry Space Group: P 21 21 21
R_factor 0.225 R_Free 0.269
length a length b length c angle alpha angle beta angle gamma
85.950 94.080 135.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.34 Å
ligand 8SU, MG enzyme
A, D, C, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (319 Kb) [Save to disk]
  • Biological Unit Coordinates (5yd6.pdb1.gz) 80 Kb
  • Biological Unit Coordinates (5yd6.pdb2.gz) 80 Kb
  • Biological Unit Coordinates (5yd6.pdb3.gz) 80 Kb
  • Biological Unit Coordinates (5yd6.pdb4.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 5YD6
  • CSU: Contacts of Structural Units for 5YD6
  • Structure Factors (1326 Kb)
  • Retrieve 5YD6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YD6 from S2C, [Save to disk]
  • View 5YD6 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 5YD6
  • 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
  • Fold representative 5yd6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yd6_D] [5yd6_C] [5yd6_B] [5yd6_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YD6
  • Community annotation for 5YD6 at PDBWiki (http://pdbwiki.org)

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