Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.11 kDa 
• Atom Count: 2566 
• Residue Count: 303 
• Unique protein chains: 3

4THN

THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE.

• DOI: 10.2210/pdb4THN/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1998-09-18 Released: 1999-06-15 
• Deposition Author(s): Lombardi, A., De Simone, G., Nastri, F., Galdiero, S., Della Morte, R., Staiano, N., Pedone, C., Bolognesi, M., Pavone, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.173 

Literature

The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.

Lombardi, A., De Simone, G., Nastri, F., Galdiero, S., Della Morte, R., Staiano, N., Pedone, C., Bolognesi, M., Pavone, V.

(1999) Protein Sci 8: 91-95

• PubMed: 10210187 
• DOI: 10.1110/ps.8.1.91
• Primary Citation of Related Structures:  
  4THN


• PubMed Abstract: 
  

The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acids, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recognition exosite through the C-terminal end. The backbone of the N-terminal tripeptide Chg1"-Arg2"-2Na13" (Chg, cyclohexyl-glycine; 2Na1, beta-(2-naphthyl)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1" side chain occupies the S2 site, Arg2" penetrates into the S1 specificity site, while the 2Na13" side chain occupies the aryl binding site. The Arg2" side chain enters the S1 specificity pocket from a position quite apart from the canonical P1 site. This notwithstanding, the Arg2" side chain establishes the typical ion pair with the carboxylate group of Asp189.

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Related Citations: 

• The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin
  Rydel, T.J., Ravichandran, K.G., Tulinsky, A., Bode, W., Huber, R., Roitsch, C., Fenton 2D, J.W.
  (1990) Science 249: 277

• Hirunorms are True Hirudin Mimetics. The Crystal Structure of Human Alpha-Thrombin-Hirunorm V Complex
  De Simone, G., Lombardi, A., Galdiero, S., Nastri, F., Della Morte, R., Staiano, N., Pedone, C., Bolognesi, M., Pavone, V.
  (1998) Protein Sci 7: 243

• Rational Design of True Hirudin Mimetics: Synthesis and Characterization of Multisite-Directed Alpha-Thrombin Inhibitors
  Lombardi, A., Nastri, F., Della Morte, R., Rossi, A., De Rosa, A., Staiano, N., Pedone, C., Pavone, V.
  (1996) J Med Chem 39: 2008

• Refined Structure of the Hirudin-Thrombin Complex
  Rydel, T.J., Tulinsky, A., Bode, W., Huber, R.
  (1991) J Mol Biol 221: 583

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Organizational Affiliation: 

Centro Interuniversitario di Ricerca su Peptidi Bioattivi & Centro di Studio di Biocristallografia-CNR, University of Napoli Federico II, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN	L	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN	H	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUNORM IV	I	26	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	I	L-PEPTIDE LINKING	C4 H9 N O2		ALA
ALC	I	L-PEPTIDE LINKING	C9 H17 N O2		ALA
NAL	I	L-PEPTIDE LINKING	C13 H13 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.3	α = 90
b = 72.7	β = 100
c = 73.6	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
CCP4	model building
TNT	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-09-18 
• Released Date: 1999-06-15 
Deposition Author(s): Lombardi, A., De Simone, G., Nastri, F., Galdiero, S., Della Morte, R., Staiano, N., Pedone, C., Bolognesi, M., Pavone, V.

Revision History 

• Version 1.0: 1999-06-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary