5E8Y | pdb_00005e8y

TGF-BETA RECEPTOR TYPE 2 KINASE DOMAIN (E431A,R433A,E485A,K488A,R493A,R495A) IN COMPLEX WITH STAUROSPORINE


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.05 Å
  • R-Value Free:&nbsp
    0.227 (Depositor), 0.230 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.197 (Depositor), 0.203 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.198&nbsp(Depositor)&nbsp

Starting Model: experimental
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Ligand Structure Quality Assessment&nbsp


This is version 1.2 of the entry. See complete&nbsphistory.&nbsp


Literature

Crystal structures of apo and inhibitor-bound TGF beta R2 kinase domain: insights into TGF beta R isoform selectivity.

Tebben, A.J.,&nbspRuzanov, M.,&nbspGao, M.,&nbspXie, D.,&nbspKiefer, S.E.,&nbspYan, C.,&nbspNewitt, J.A.,&nbspZhang, L.,&nbspKim, K.,&nbspLu, H.,&nbspKopcho, L.M.,&nbspSheriff, S.

(2016) Acta Crystallogr D Struct Biol&nbsp72: 658-674

  • DOI:&nbsphttps://doi.org/10.1107/S2059798316003624
  • Primary Citation Related Structures:&nbsp
    5E8S, 5E8T, 5E8U, 5E8V, 5E8W, 5E8X, 5E8Y, 5E8Z, 5E90, 5E91, 5E92

  • PubMed Abstract:&nbsp

    The cytokine TGF-β modulates a number of cellular activities and plays a critical role in development, hemostasis and physiology, as well as in diseases including cancer and fibrosis. TGF-β signals through two transmembrane serine/threonine kinase receptors: TGFβR1 and TGFβR2. Multiple structures of the TGFβR1 kinase domain are known, but the structure of TGFβR2 remains unreported. Wild-type TGFβR2 kinase domain was refractory to crystallization, leading to the design of two mutated constructs: firstly, a TGFβR1 chimeric protein with seven ATP-site residues mutated to their counterparts in TGFβR2, and secondly, a reduction of surface entropy through mutation of six charged residues on the surface of the TGFβR2 kinase domain to alanines. These yielded apo and inhibitor-bound crystals that diffracted to high resolution (<2 Å). Comparison of these structures with those of TGFβR1 reveal shared ligand contacts as well as differences in the ATP-binding sites, suggesting strategies for the design of pan and selective TGFβR inhibitors.


  • Organizational Affiliation:&nbsp
    • Molecular Structure and Design, Bristol-Myers Squibb R & D, PO Box 4000, Princeton, NJ 08543-4000, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TGF-beta receptor type-2316Homo sapiensMutation(s): 6&nbsp
Gene Names:&nbspTGFBR2
EC:&nbsp2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP37173&nbsp(Homo sapiens)
Explore&nbspP37173&nbsp
Go to UniProtKB: &nbspP37173
PHAROS: &nbspP37173
GTEx: &nbspENSG00000163513&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37173
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands&nbsp1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STU
Query on STU

Download Ideal Coordinates CCD File&nbsp
B [auth A]STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.05 Å
  • R-Value Free:&nbsp 0.227 (Depositor), 0.230 (DCC)&nbsp
  • R-Value Work:&nbsp 0.197 (Depositor), 0.203 (DCC)&nbsp
  • R-Value Observed:&nbsp0.198&nbsp(Depositor)&nbsp
Space Group:&nbspP 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.9α = 90
b = 75.97β = 90
c = 74.98γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing

Structure Validation

View&nbspFull Validation Report



Ligand Structure Quality Assessment&nbsp


Entry History&nbsp

Deposition Data

  • Released Date:&nbsp2016-05-11&nbsp
  • Deposition Author(s):&nbspSheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description