1YOK Transcription date Jan 27, 2005
title Crystal Structure Of Human Lrh-1 Bound With Tif-2 Peptide And Phosphatidylglycerol
authors I.N.Krylova, E.P.Sablin, J.Moore, R.X.Xu, G.M.Waitt, J.A.Mackay, D.Juzumiene, J.M.Bynum, K.Madauss, V.Montana, L.Lebedeva, M.Suzawa, J.D.Williams, S.P.Williams, R.K.Guy, J.W.Thornton, R.J.Fletterick, T.M.Willson, H.A.Ingraham
compound source
Molecule: Orphan Nuclear Receptor Nr5a2
Chain: A
Fragment: Sequence Database Residues 300-541: Contains Ligand Binding Domain (Residues 346-388);
Synonym: Alpha-1-Fetoprotein Transcription Factor, Hepatocytic Transcription Factor, B1-Binding Factor, Hb1f, Cyp7a Promoter Binding Factor;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr5a2, B1f, Cpf, Ftf
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Nuclear Receptor Coactivator 2
Chain: B, C
Fragment: Sequence Database Residues 740-753
Synonym: Ncoa-2, Transcriptional Intermediary Factor 2
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. The Sequence Of The Peptide Is Naturally Found In Homo Sapiens (Human).
symmetry Space Group: P 21 21 21
R_factor 0.230 R_Free 0.290
length a length b length c angle alpha angle beta angle gamma
59.938 67.199 79.569 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand P6L enzyme

Primary referenceStructural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1., Krylova IN, Sablin EP, Moore J, Xu RX, Waitt GM, MacKay JA, Juzumiene D, Bynum JM, Madauss K, Montana V, Lebedeva L, Suzawa M, Williams JD, Williams SP, Guy RK, Thornton JW, Fletterick RJ, Willson TM, Ingraham HA, Cell 2005 Feb 11;120(3):343-55. PMID:15707893
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (1yok.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 1YOK
  • CSU: Contacts of Structural Units for 1YOK
  • Likely Quarternary Molecular Structure file(s) for 1YOK
  • Structure Factors (164 Kb)
  • Retrieve 1YOK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YOK from S2C, [Save to disk]
  • Re-refined 1yok structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YOK 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 1YOK
  • 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
  • 3D motif for 1YOK, from MSDmotif at EBI
  • Fold representative 1yok from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yok] [1yok_B] [1yok_C] [1yok_A]
  • SWISS-PROT database: [Q15596] [O00482]
  • Domain organization of [NCOA2_HUMAN] [NR5A2_HUMAN] by SWISSPFAM
  • Domain found in 1YOK: [HOLI ] by SMART
  • Other resources with information on 1YOK
  • Community annotation for 1YOK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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