Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39070.77 
• Atom Count: 2685 
• Residue Count: 310 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

1HUT

THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER

• DOI: 10.2210/pdb1HUT/pdb
• NDB: PDE013

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


• Deposited: 1993-05-27 Released: 1994-06-22 
• Deposition Author(s): Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., Sadler, J.E., Tulinsky, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Work: 0.159 

Literature

The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.

Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., Sadler, J.E., Tulinsky, A.

(1993) J.Biol.Chem. 268: 17651-17654

• PubMed: 8102368 
• Also Cited By: 4DII, 4DIH


• PubMed Abstract: 
  

The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets. The DNA is sandwiched between two different positively charged regions of two symmetry-related thrombin molecules in the crystal structure making ionic and hydrophobic interactions. One region is the fibrinogen recognition exosite and the other, the putative heparin binding site. The lack of inhibition of fibrinogen clotting and platelet activation by the DNA 15-mer with the Arg75-->Glu mutant of thrombin is consistent with the several salt bridges of the DNA in the fibrinogen exosite. The association of DNA with the heparin site of a neighboring molecule appears to simply compensate residual charge. Differences in the 15-mer loop conformations between the complex and NMR solution structures can be attributed to conformational changes upon thrombin binding. Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the latter in the thrombin complex.

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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: 2
Molecule	Chains	Sequence Length	Organism	Details
ALPHA-Thrombin light chain	L	36	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
ALPHA-Thrombin heavy chain	H	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: 1
Molecule	Chains	Length	Organism
DNA 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'	D	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
0G7	H	D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide d-Phe-Pro-Arg chloromethylketone (PPACK) C21 H31 Cl N6 O3 KWPACVJPAFGBEQ-IKGGRYGDSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000021 (0G7)	H	D-Phe-Pro-Arg chloromethylketone (PPACK)	Peptide-like / Inhibitor		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0G7	IC50: 1.5 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Work: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.520	α = 90.00
b = 77.440	β = 90.00
c = 99.520	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-05-27 
• Released Date: 1994-06-22 
• Deposition Author(s): Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., Sadler, J.E., Tulinsky, A.

Revision History 

• Version 1.0: 1994-06-22
  Type: Initial release
• Version 1.1: 2008-05-22
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-07-27
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2013-02-27
  Type: Other