1GA5	Transcription Dna	date	Nov 29, 2000
title	Crystal Structure Of The Orphan Nuclear Receptor Rev-Erb(Alp Binding Domain Bound To Its Cognate Response Element
authors	M.L.Sierk, Q.Zhao, F.Rastinejad
compound		source
Molecule: 5'-D(Cpapapcptpapgpgptpcpapcptpapg Apg)-3'; Chain: C, G Engineered: Yes		Synthetic: Yes Other_details: Synthesized Optimal Dr2 Target
Molecule: 5'-D(Cptpgpapcpcptpapgptpgpapcpcpt (5it)Pg)-3'; Chain: D, H Engineered: Yes		Synthetic: Yes Other_details: Synthesized Optimal Dr2 Target Complementary With 5-Iodo-Thymidine;
Molecule: Orphan Nuclear Receptor Nr1d1 Chain: A, B, E, F Fragment: Dna-Binding Domain Plus C-Terminal Extension Synonym: Rev-Erb(Alpha) Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Nr1d1 Or Thral Or Ear1 Or Hrev Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex
symmetry	Space Group: P 1	R_factor 0.253 R_Free 0.299
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.920 52.020 78.880 85.84 76.61 74.48
method	X-Ray Diffraction	resolution	2.40 Å
ligand	5IU, ZN	enzyme
related structures	by homologous chain: 1A6Y, 1HLZ
Gene Ontology	Chain Function Process Component F, A, E, B
Primary reference	DNA deformability as a recognition feature in the reverb response element., Sierk ML, Zhao Q, Rastinejad F, Biochemistry 2001 Oct 30;40(43):12833-43. PMID:11669620

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk] Biological Unit Coordinates (1ga5.pdb1.gz) 44 Kb Biological Unit Coordinates (1ga5.pdb2.gz) 44 Kb LPC: Ligand-Protein Contacts for 1GA5 CSU: Contacts of Structural Units for 1GA5 Likely Quarternary Molecular Structure file(s) for 1GA5 Structure Factors (223 Kb) Retrieve 1GA5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1GA5 from S2C, [Save to disk] Re-refined 1ga5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1GA5 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 1GA5

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 3D motif for 1GA5, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ga5a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1ga5b_, region B [Jmol] [rasmolscript] [script source]     - Domain d1ga5e_, region E [Jmol] [rasmolscript] [script source]     - Domain d1ga5f_, region F [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ga5_B] [1ga5_F] [1ga5_H] [1ga5_E] [1ga5_C] [1ga5_G] [1ga5_D] [1ga5] [1ga5_A] SWISS-PROT database: [P20393] Domain organization of [NR1D1_HUMAN] by SWISSPFAM Domain found in 1GA5: [ZnF_C4 ] by SMART

Other resources with information on 1GA5

Community annotation for 1GA5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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