Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.63 kDa 
• Atom Count: 2581 
• Residue Count: 285 
• Unique protein chains: 3

1BCU

ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND PROFLAVIN

• DOI: 10.2210/pdb1BCU/pdb

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


• Deposited: 1998-05-02 Released: 1998-10-14 
• Deposition Author(s): Conti, E., Rivetti, C., Wonacott, A., Brick, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

X-ray and spectrophotometric studies of the binding of proflavin to the S1 specificity pocket of human alpha-thrombin.

Conti, E., Rivetti, C., Wonacott, A., Brick, P.

(1998) FEBS Lett 425: 229-233

• PubMed: 9559654 
• DOI: 10.1016/s0014-5793(98)00235-x
• Primary Citation of Related Structures:  
  1BCU


• PubMed Abstract: 
  

Proflavin can be used to study the interactions of inhibitors and substrates with thrombin by monitoring the changes in the visible absorption spectrum that occur on dye displacement. We have used microspectrophotometric methods to investigate the binding of proflavin to crystals of an alpha-thrombin-hirugen complex and have determined the structure by X-ray crystallography. The proflavin molecule binds in the S1 pocket of the enzyme with one of the amino groups hydrogen bonded to the carboxylate of Asp-189 while the protonated ring nitrogen is hydrogen bonded to the carbonyl of Gly-219. This result indicates that the proflavin displacement assay can be used to specifically monitor the binding of inhibitors to the S1 pocket.

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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

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Organizational Affiliation: 

Blackett Laboratory, Imperial College, London, UK.

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
HIRUGEN	I	12	Hirudo medicinalis	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
PRL	H	PROFLAVIN C13 H11 N3 WDVSHHCDHLJJJR-UHFFFAOYSA-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 %)
PRL	Kd:  530000   nM  Binding MOAD
PRL	Kd :  530000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.15	α = 90
b = 72.25	β = 100.61
c = 72.67	γ = 90

Software Package:

Software Name	Purpose
MADNES	data collection
CCP4	data reduction
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-05-02 
• Released Date: 1998-10-14 
Deposition Author(s): Conti, E., Rivetti, C., Wonacott, A., Brick, P.

Revision History 

• Version 1.0: 1998-10-14
  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: 2018-04-18
  Changes: Data collection, Other