5ODG Transcription date Jul 05, 2017
title Crystal Structure Of Smad3-Mh1 Bound To The Ggct Site.
authors Z.Kaczmarska, J.A.Marquez, M.J.Macias
compound source
Molecule: Mothers Against Decapentaplegic Homolog 3
Chain: A, B
Fragment: Mh1 Domain, Unp Residues 11-135
Synonym: Hmad-3,Jv15-2,Smad Family Member 3,Hsmad3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Smad3, Madh3
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Pcpapgpgpcptpapgpcpcptpgpc
Chain: D, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: I 41
R_factor 0.199 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.990 104.990 72.490 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.12 Å
ligand CL, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors., Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ, Nat Commun. 2017 Dec 12;8(1):2070. doi: 10.1038/s41467-017-02054-6. PMID:29234012
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (5odg.pdb1.gz) 111 Kb
  • Biological Unit Coordinates (5odg.pdb2.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 5ODG
  • CSU: Contacts of Structural Units for 5ODG
  • Structure Factors (754 Kb)
  • Retrieve 5ODG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ODG from S2C, [Save to disk]
  • View 5ODG 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 5ODG
  • 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
  • Fold representative 5odg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5odg_B] [5odg_D] [5odg_E] [5odg_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5ODG
  • Community annotation for 5ODG at PDBWiki (http://pdbwiki.org)

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