1MHD Complex (Transcription Activator Dna) date Aug 18, 1998
title Crystal Structure Of A Smad Mh1 Domain Bound To Dna
authors Y.Shi
compound source
Molecule: Dna
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Dna
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Smad3
Chain: A, B
Fragment: Mh1 Domain, Residues 1 - 144
Synonym: Smad N-Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cellular_location: Cytoplasm
Gene: Smad
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_cellular_location: Cytoplasm
Expression_system_vector_type: Plasmid
Expression_system_vector: Pgex-2t
Expression_system_plasmid: Pgex
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.600 60.400 71.600 90.00 102.00 90.00
method X-Ray Diffractionresolution 2.80 Å
related structures by homologous chain: 1OZJ
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling., Shi Y, Wang YF, Jayaraman L, Yang H, Massague J, Pavletich NP, Cell 1998 Sep 4;94(5):585-94. PMID:9741623
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (1mhd.pdb1.gz) 54 Kb
  • CSU: Contacts of Structural Units for 1MHD
  • Likely Quarternary Molecular Structure file(s) for 1MHD
  • Retrieve 1MHD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MHD from S2C, [Save to disk]
  • View 1MHD 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 1MHD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1MHD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1mhda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1mhdb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1mhd 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: [1mhd_B] [1mhd] [1mhd_C] [1mhd_D] [1mhd_A]
  • SWISS-PROT database: [P84022]
  • Domain organization of [SMAD3_HUMAN] by SWISSPFAM
  • Domain found in 1MHD: [DWA ] by SMART
  • Alignments of the sequence of 1MHD with the sequences similar proteins can be viewed for 1MHD's classification [SMAD3_HUMAN] 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 [SMAD3_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1MHD
  • Community annotation for 1MHD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science