Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68992.96 
• Atom Count: 4635 
• Residue Count: 591 
• Unique protein chains: 3

1HLT

THE STRUCTURE OF A NONADECAPEPTIDE OF THE FIFTH EGF DOMAIN OF THROMBOMODULIN COMPLEXED WITH THROMBIN

• DOI: 10.2210/pdb1HLT/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 1994-08-28 Released: 1994-12-20 
• Deposition Author(s): Tulinsky, A., Mathews, I.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Work: 0.146 

Literature

Structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin complexed with thrombin.

Mathews, I.I., Padmanabhan, K.P., Tulinksy, A., Sadler, J.E.

(1994) Biochemistry 33: 13547-13552

• PubMed: 7947765 


• PubMed Abstract: 
  

The crystallographic structure has been determined of a complex between a nonadecapeptide from the fifth epidermal growth factor (EGF5) domain of human thrombomodulin and human D-PheProArg-alpha-thrombin. The peptide corresponds to amino acid residues Glu408-Glu426 of thrombomodulin and contains the third disulfide loop of EGF5 and its linker to EGF6. The structure was refined at 3.0-A resolution to an R-value of 0.146. There are two thrombin molecules in the asymmetric unit, and the structure in the crystal is a 2:1 thrombin complex. The folding of the peptide corresponds closely to the third disulfide loop of EGF2 of factor Xa (rms delta = 1.0 A). The peptide is squeezed between cofacial electropositive fibrinogen recognition exo sites of the two thrombin molecules. Since the peptide has a total of seven aspartic and glutamic acid residues, the principal binding interaction with thrombin is electrostatic. A major hydrophobic association, which is highly directional in such a pronounced electrostatic environment, involves a TyrIleLeu triplet of the peptide and Phe34, Leu65, Tyr76, and Ile82 (chymotrypsinogen numbering) of one thrombin molecule. The tyrosine of the peptide is sandwiched between the thrombin aromatic rings and is most likely the prime source of the specificity of the thrombomodulin-thrombin interaction.

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Related Citations: 

• Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
  Skrzypczak-Jankun, E.,Carperos, V.E.,Ravichandran, K.G.,Tulinsky, A.,Westbrook, M.,Maraganore, J.M.
  (1991) J.Mol.Biol. 221: 1379
• Alanine-Scanning Mutagenesis of the Epidermal Growth Factor-Like Domains of Human Thrombomodulin Identifies Critical Residues for its Cofactor Activity
  Nagashima, M.,Lundh, E.,Leonard, J.C.,Parkinson, J.F.
  (1993) J.Biol.Chem. 268: 2888




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Organizational Affiliation: 

Department of Chemistry, Michigan State University, East Lansing 48824-1322.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALPHA-THROMBIN (SMALL SUBUNIT)	L, J	27	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ALPHA-THROMBIN (LARGE SUBUNIT)	H, K	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Thrombomodulin	R	19	Homo sapiens	Mutation(s): 0  Gene Names: THBD (THRM)
Find proteins for P07204 (Homo sapiens) Go to Gene View: THBD Go to UniProtKB:  P07204

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
0G6	H, K	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide PPACK C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6)	H,K	D-Phe-Pro-Arg-CH2Cl	Peptide-like / Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Work: 0.146 
• Space Group: P 4₃

Unit Cell:

Length (Å)	Angle (°)
a = 50.900	α = 90.00
b = 50.900	β = 90.00
c = 325.800	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-08-28 
• Released Date: 1994-12-20 
• Deposition Author(s): Tulinsky, A., Mathews, I.I.

Revision History 

• Version 1.0: 1994-12-20
  Type: Initial release
• Version 1.1: 2008-03-07
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Type: Other