Crystal Structure of the Thrombospondin-1 Type 1 Repeats

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Crystal structure of the TSP-1 type 1 repeats: a novel layered fold and its biological implication.

Tan, K.Duquette, M.Liu, J.H.Dong, Y.Zhang, R.Joachimiak, A.Lawler, J.Wang, J.H.

(2002) J Cell Biol 159: 373-382

  • DOI: https://doi.org/10.1083/jcb.200206062
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Thrombospondin-1 (TSP-1) contains three type 1 repeats (TSRs), which mediate cell attachment, glycosaminoglycan binding, inhibition of angiogenesis, activation of TGFbeta, and inhibition of matrix metalloproteinases. The crystal structure of the TSRs reported in this article reveals a novel, antiparallel, three-stranded fold that consists of alternating stacked layers of tryptophan and arginine residues from respective strands, capped by disulfide bonds on each end. The front face of the TSR contains a right-handed spiral, positively charged groove that might be the "recognition" face, mediating interactions with various ligands. This is the first high-resolution crystal structure of a TSR domain that provides a prototypic architecture for structural and functional exploration of the diverse members of the TSR superfamily.

  • Organizational Affiliation

    Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombospondin 1113Homo sapiensMutation(s): 0 
Gene Names: THBS1TSPTSP1
UniProt & NIH Common Fund Data Resources
Find proteins for P07996 (Homo sapiens)
Explore P07996 
Go to UniProtKB:  P07996
PHAROS:  P07996
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07996
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FUC

Download Ideal Coordinates CCD File 
C [auth A]alpha-L-fucopyranose
C6 H12 O5
Query on FUL

Download Ideal Coordinates CCD File 
B [auth A]beta-L-fucopyranose
C6 H12 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.63α = 90
b = 84.41β = 108.67
c = 37.17γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary