Macromolecule Content

• Total Structure Weight: 2018.18 
• Atom Count: 140 
• Residue Count: 18 
• Unique protein chains: 1

1FGD

EPIDERMAL GROWTH FACTOR (EGF) SUBDOMAIN OF HUMAN THROMBOMODULIN (NMR, 11 STRUCTURES)

• DOI: 10.2210/pdb1FGD/pdb

• Classification: BLOOD COAGULATION INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 1995-11-28 Released: 1996-06-20 
• Deposition Author(s): Hrabal, R., Komives, E.A., Ni, F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 11 

Literature

Structural resiliency of an EGF-like subdomain bound to its target protein, thrombin.

Hrabal, R., Komives, E.A., Ni, F.

(1996) Protein Sci. 5: 195-203

• PubMed: 8745396 
• DOI: 10.1002/pro.5560050202
• Primary Citation of Related Structures:  
  1FGE


• PubMed Abstract: 
  

The thrombin-bound structures of native peptide fragments from the fifth EGF-like domain of thrombomodulin were determined by use of NMR and transferred NOE spectroscopy. The bound peptides assume an EGF-like structure of an antiparallel beta-sheet, a novel structural motif observed for a bound peptide in protein-peptide complexes. There is a remarkable structural resiliency of this structure motif manifested in its ability to accommodate a different number of residues within the disulfide loop. Docking experiments revealed that the key contacts with thrombin are hydrophobic interactions between the side chains of residues Ile 414 and Ile 424 of thrombomodulin and a hydrophobic pocket on the thrombin surface. Residues Leu 415, Phe 419, and Ile 420, which would have been buried in intact EGF-like domains, are unfavorably exposed in the complex of thrombin with the EGF-like thrombomodulin fragment, thus providing a rationale for the enhancement of binding affinity upon the deletion of Ile 420. The unique beta-sheet structures of the bound peptides are specified by the presence of disulfide bridges in the peptides because a corresponding linear thrombomodulin fragment folds into a sheet structure with a different backbone topology. The different bound conformations for the linear and the cyclized peptides indicate that side-chain interactions within a specific environment may dictate the folding of bound peptides in protein-peptide complexes.

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Organizational Affiliation: 

Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
THROMBOMODULIN	A	18	Homo sapiens	Mutation(s): 0  Gene Names: THBD (THRM)
Find proteins for P07204 (Homo sapiens) Go to Gene View: THBD Go to UniProtKB:  P07204

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 11 
• Olderado: 1FGD Olderado

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-11-28 
• Released Date: 1996-06-20 
• Deposition Author(s): Hrabal, R., Komives, E.A., Ni, F.

Revision History 

• Version 1.0: 1996-06-20
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance