Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.72 kDa 
• Atom Count: 2600 
• Residue Count: 289 
• Unique protein chains: 3

1AHT

CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND P-AMIDINOPHENYLPYRUVATE AT 1.6 ANGSTROMS RESOLUTION

• DOI: 10.2210/pdb1AHT/pdb

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


• Deposited: 1995-03-17 Released: 1996-03-17 
• Deposition Author(s): Chen, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Literature

Crystal structure of human alpha-thrombin complexed with hirugen and p-amidinophenylpyruvate at 1.6 A resolution.

Chen, Z., Li, Y., Mulichak, A.M., Lewis, S.D., Shafer, J.A.

(1995) Arch Biochem Biophys 322: 198-203

• PubMed: 7574675 
• DOI: 10.1006/abbi.1995.1452
• Primary Citation of Related Structures:  
  1AHT


• PubMed Abstract: 
  

Crystals of human alpha-thrombin complexed with hirugen and the alpha-keto acid thrombin inhibitor APPA (p-amidinophenylpyruvate) that diffract to 1.6 A resolution were obtained by soaking an alpha-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an R factor of 18.7% at 1.6 A resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with O gamma of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin.

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Organizational Affiliation: 

Department of Biological Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN (SMALL SUBUNIT)	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 (LARGE SUBUNIT)	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
HIRUGEN	I	13	N/A	Mutation(s): 0
Find proteins for P01050 (Hirudo medicinalis) Explore P01050  Go to UniProtKB:  P01050

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APA	H	(2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid C10 H12 N2 O3 FAFAPKBWTCDDJC-QMMMGPOBSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	I	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
APA	Ki :  620   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.24	α = 90
b = 72.39	β = 101.01
c = 73.06	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-03-17 
• Released Date: 1996-03-17 
Deposition Author(s): Chen, Z.

Revision History 

• Version 1.0: 1996-03-17
  Type: Initial release
  
• Version 1.1: 2008-03-03
  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: 2011-11-16
  Changes: Atomic model