6FZT

Crystal structure of Smad8_9-MH1 bound to the GGCGC site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Recognition of the 5GC DNA motif is conserved in BMP and TGF-beta activated Smad proteins

Ruiz, L.Kaczmarska, Z.Aragon, E.Cordero, J.Martin Malpartida, P.Freier, R.Marquez, J.A.Macias, M.J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mothers against decapentaplegic homolog 9
A, B
140Homo sapiensMutation(s): 0 
Gene Names: SMAD9 (MADH6, MADH9, SMAD8)
Find proteins for O15198 (Homo sapiens)
Go to Gene View: SMAD9
Go to UniProtKB:  O15198
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3')C,D16Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.433α = 90.00
b = 79.509β = 90.00
c = 88.372γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
XDSdata reduction
AutoPROCdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionGermanyEMBL_291772
European CommissionSpainIRBPostPro2.0_600404
Ministry of Economy and CompetitivenessSpainBFU2014-53787-P
European CommissionFrance653706

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release