5Y41 Transcription date Jul 31, 2017
title Crystal Structure Of Ligand-Bound Nurr1-Lbd
authors R.Sreekanth, J.Lescar, H.S.Yoon
compound source
Molecule: Nuclear Receptor Subfamily 4 Group A Member 2
Chain: A, B
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 2
R_factor 0.206 R_Free 0.253
length a length b length c angle alpha angle beta angle gamma
88.520 131.460 47.130 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand CL, MG, PEG, PGE, RPG enzyme
A, B

Primary referencePGE1 and PGA1 bind to Nurr1 and activate its transcriptional function., Rajan S, Jang Y, Kim CH, Kim W, Toh HT, Jeon J, Song B, Serra A, Lescar J, Yoo JY, Beldar S, Ye H, Kang C, Liu XW, Feitosa M, Kim Y, Hwang D, Goh G, Lim KL, Park HM, Lee CH, Oh SF, Petsko GA, Yoon HS, Kim KS, Nat Chem Biol. 2020 May 25. pii: 10.1038/s41589-020-0553-6. doi:, 10.1038/s41589-020-0553-6. PMID:32451509
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk]
  • Biological Unit Coordinates (5y41.pdb1.gz) 82 Kb
  • Biological Unit Coordinates (5y41.pdb2.gz) 83 Kb
  • Biological Unit Coordinates (5y41.pdb3.gz) 163 Kb
  • LPC: Ligand-Protein Contacts for 5Y41
  • CSU: Contacts of Structural Units for 5Y41
  • Structure Factors (979 Kb)
  • Retrieve 5Y41 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y41 from S2C, [Save to disk]
  • View 5Y41 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 5Y41
  • 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 5y41 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y41_A] [5y41_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Y41
  • Community annotation for 5Y41 at PDBWiki (http://pdbwiki.org)

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