4DQM Transcription Transferase date Feb 16, 2012
title Revealing A Marine Natural Product As A Novel Agonist For Re Acid Receptors With A Unique Binding Mode And Antitumor Act
authors S.Wang, Z.Wang, S.Lin, W.Zheng, R.Wang, S.Jin, J.Chen, L.Jin, Y.Li
compound source
Molecule: Retinoic Acid Receptor Alpha
Chain: A, C
Fragment: Ligand Binding Domain, Unp Residues 182-415
Synonym: Rar-Alpha, Nuclear Receptor Subfamily 1 Group B Me
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr1b1, Rara
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24a

Molecule: Nuclear Receptor Coactivator 1
Chain: B, D
Fragment: Lxxll Motif 7, Unp Residues 1432-1441
Synonym: Ncoa-1, Class E Basic Helix-Loop-Helix Protein 74, Protein Hin-2, Rip160, Renal Carcinoma Antigen Ny-Ren-52, S Receptor Coactivator 1, Src-1;
Ec: 2.3.1.48
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 2 21 21
R_factor 0.213 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.120 104.460 113.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand LUF enzyme Transferase E.C.2.3.1.48 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceRevealing a natural marine product as a novel agonist for retinoic acid receptors with a unique binding mode and inhibitory effects on cancer cells., Wang S, Wang Z, Lin S, Zheng W, Wang R, Jin S, Chen J, Jin L, Li Y, Biochem J. 2012 Aug 15;446(1):79-87. PMID:22642567
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (4dqm.pdb1.gz) 42 Kb
  • Biological Unit Coordinates (4dqm.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 4DQM
  • CSU: Contacts of Structural Units for 4DQM
  • Structure Factors (275 Kb)
  • Retrieve 4DQM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DQM from S2C, [Save to disk]
  • Re-refined 4dqm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DQM 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 4DQM
  • 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 4DQM, from MSDmotif at EBI
  • Fold representative 4dqm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dqm_A] [4dqm] [4dqm_B] [4dqm_C] [4dqm_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4DQM with the sequences similar proteins can be viewed for 4DQM'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 4DQM
  • Community annotation for 4DQM at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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