1DD1 Signaling Protein date Nov 05, 1999
title Crystal Structure Analysis Of The Smad4 Active Fragment
authors B.Y.Qin, S.W.Lam, K.Lin
compound source
Molecule: Smad4
Chain: A, B, C
Fragment: Smad4 Active Fragment
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: I 41 2 2
R_factor 0.218 R_Free 0.175
crystal
cell
length a length b length c angle alpha angle beta angle gamma
142.433 142.433 195.478 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.62 Å
ligand SO4 enzyme
related structures by homologous chain: 1U7F, 1U7V
Primary referenceCrystal structure of a transcriptionally active Smad4 fragment., Qin B, Lam SS, Lin K, Structure Fold Des 1999 Dec 15;7(12):1493-503. PMID:10647180
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (1dd1.pdb1.gz) 119 Kb
  • Biological Unit Coordinates (1dd1.pdb2.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 1DD1
  • CSU: Contacts of Structural Units for 1DD1
  • Likely Quarternary Molecular Structure file(s) for 1DD1
  • Structure Factors (238 Kb)
  • Retrieve 1DD1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DD1 from S2C, [Save to disk]
  • Re-refined 1dd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DD1 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 1DD1
  • 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 1DD1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dd1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dd1b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1dd1c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1k1dd1, region D:1-52,D:385-460 [Jmol] [rasmolscript] [script source]
  • Fold representative 1dd1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1dd1_C] [1dd1] [1dd1_A] [1dd1_B]
  • SWISS-PROT database: [Q13485]
  • Domain organization of [SMAD4_HUMAN] by SWISSPFAM
  • Domain found in 1DD1: [DWB ] by SMART
  • Other resources with information on 1DD1
  • Community annotation for 1DD1 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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