1OQJ Dna Binding Protein date Mar 10, 2003
title Crystal Structure Of The Sand Domain From Glucocorticoid Mod Element Binding Protein-1 (Gmeb1)
authors P.L.Surdo, M.J.Bottomley, M.Sattler, K.Scheffzek
compound source
Molecule: Glucocorticoid Modulatory Element Binding Protein
Chain: A, B
Fragment: Sand Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gmeb1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet24d With N-His-Tev C Site
symmetry Space Group: P 21 21 21
R_factor 0.194 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.946 49.077 88.903 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand ZN enzyme
note 1OQJ is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure and nuclear magnetic resonance analyses of the SAND domain from glucocorticoid modulatory element binding protein-1 reveals deoxyribonucleic acid and zinc binding regions., Surdo PL, Bottomley MJ, Sattler M, Scheffzek K, Mol Endocrinol 2003 Jul;17(7):1283-95. PMID:12702733
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (1oqj.pdb1.gz) 17 Kb
  • Biological Unit Coordinates (1oqj.pdb2.gz) 17 Kb
  • LPC: Ligand-Protein Contacts for 1OQJ
  • CSU: Contacts of Structural Units for 1OQJ
  • Likely Quarternary Molecular Structure file(s) for 1OQJ
  • Structure Factors (237 Kb)
  • Retrieve 1OQJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OQJ from S2C, [Save to disk]
  • Re-refined 1oqj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1OQJ 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 1OQJ
  • 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 1OQJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1oqja_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1oqjb_, region B [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: [1oqj_B] [1oqj] [1oqj_A]
  • SWISS-PROT database: [Q9Y692]
  • Domain organization of [GMEB1_HUMAN] by SWISSPFAM
  • Domain found in 1OQJ: [SAND ] by SMART
  • Other resources with information on 1OQJ
  • Community annotation for 1OQJ 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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