3B1M Transcription date Jul 05, 2011
title Crystal Structure Of The Ppargamma-Lbd Complexed With A Cerc Derivative Modulator Cerco-A
authors Y.Matsui, H.Hiroyuki
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: A
Fragment: Ligand Binding Domain, Unp Residues 234-505
Synonym: Ppar-Gamma, Nuclear Receptor Subfamily 1 Group C M
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pparg, Nr1c3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe-30

Molecule: Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-Alpha;
Chain: B
Fragment: Peptide Containing Lxxll Box, Unp Residues 136-15
Synonym: Pgc-1-Alpha, Ppar-Gamma Coactivator 1-Alpha, Pparg Ligand Effect Modulator 6;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Sequence Occurs Naturally In Humans.
symmetry Space Group: P 1 21 1
R_factor 0.217 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.946 54.622 66.782 90.00 92.21 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand KRC BindingDB enzyme
Primary referencePharmacology and in vitro profiling of a novel peroxisome proliferator-activated receptor gamma ligand, Cerco-A., Wakabayashi K, Hayashi S, Matsui Y, Matsumoto T, Furukawa A, Kuroha M, Tanaka N, Inaba T, Kanda S, Tanaka J, Okuyama R, Wakimoto S, Ogata T, Araki K, Ohsumi J, Biol Pharm Bull. 2011;34(7):1094-104. PMID:21720019
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (3b1m.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3B1M
  • CSU: Contacts of Structural Units for 3B1M
  • Structure Factors (411 Kb)
  • Retrieve 3B1M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B1M from S2C, [Save to disk]
  • Re-refined 3b1m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3B1M 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 3B1M
  • 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 3B1M, from MSDmotif at EBI
  • Fold representative 3b1m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b1m_A] [3b1m_B] [3b1m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3B1M: [HOLI ] by SMART
  • Alignments of the sequence of 3B1M with the sequences similar proteins can be viewed for 3B1M's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3B1M
  • Community annotation for 3B1M at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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