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 5E8Y|pdb_00005e8y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

Tebben, A.J.Ruzanov, M.Gao, M.Xie, D.Kiefer, S.E.Yan, C.Newitt, J.A.Zhang, L.Kim, K.Lu, H.Kopcho, L.M.Sheriff, S.

(2016) Acta Crystallogr D Struct Biol 72: 658-674

  • PubMed27139629 Search on PubMed
  • DOI: https://doi.org/10.1107/S2059798316003624
  • Primary Citation of Related Structures:  
    5E8S,5E8T,5E8U,5E8V,5E8W,5E8X,5E8Y,5E8Z,5E90,5E91,5E92

  • PubMed Abstract: 

    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
    • Molecular Structure and Design, Bristol-Myers Squibb R & D, PO Box 4000, Princeton, NJ 08543-4000, USA.
    • Protein Science, Bristol-Myers Squibb R & D, PO Box 4000, Princeton, NJ 08543-4000, USA.
    • Discovery Chemistry Oncology, Bristol-Myers Squibb R & D, PO Box 4000, Princeton, NJ 08543-4000, USA.
    • Mechanistic Biochemistry, Bristol-Myers Squibb R & D, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (STU)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

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Macromolecule Content 

  • Total Structure Weight: 36.31 kDa 
  • Atom Count: 2,385 
  • Modeled Residue Count: 298 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TGF-beta receptor type-2316Homo sapiensMutation(s): 6 
Gene Names: TGFBR2
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P37173 (Homo sapiens)
Explore P37173 
Go to UniProtKB:  P37173
PHAROS:  P37173
GTEx:  ENSG00000163513 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37173
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STU
Query on STU

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 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 Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-05-11 
  • Deposition Author(s): Sheriff, 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
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


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