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: 34.58 kDa 
• Atom Count: 2658 
• Residue Count: 294 
• Unique protein chains: 3

3BV9

Structure of Thrombin Bound to the Inhibitor FM19

• DOI: 10.2210/pdb3BV9/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2008-01-05 Released: 2008-03-04 
• Deposition Author(s): Nieman, M.T., Burke, F., Warnock, M., Zhou, Y., Sweigert, J., Chen, A., Ricketts, D., Lucchesi, B.R., Chen, Z., Di Cera, E., Hilfinger, J., Mosberg, H.I., Schmaier, A.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Literature

Thrombostatin FM compounds: direct thrombin inhibitors - mechanism of action in vitro and in vivo.

Nieman, M.T., Burke, F., Warnock, M., Zhou, Y., Sweigart, J., Chen, A., Ricketts, D., Lucchesi, B.R., Chen, Z., Di Cera, E., Hilfinger, J., Kim, J.S., Mosberg, H.I., Schmaier, A.H.

(2008) J Thromb Haemost 6: 837-845

• PubMed: 18315550 
• DOI: 10.1111/j.1538-7836.2008.02937.x
• Primary Citation of Related Structures:  
  3BV9


• PubMed Abstract: 
  

Novel pentapeptides called Thrombostatin FM compounds consisting mostly of D-isomers and unusual amino acids were prepared based upon the stable angiotensin converting enzyme breakdown product of bradykinin - RPPGF.

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Related Citations: 

• Molecular dissection of Na+ binding to thrombin.
  Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S., Di Cera, E.
  (2004) J Biol Chem 279: 31842

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Organizational Affiliation: 

Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106-7284, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A	31	N/A	Mutation(s): 0  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
Thrombin heavy chain	B	259	Homo sapiens	Mutation(s): 1  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
FM19 inhibitor	C	6	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	B	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4PH	C	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000276	C	Thrombostatin FM inhibitor [rOicPaF(p-Me)]	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.907	α = 90
b = 80.907	β = 90
c = 183.718	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-05 
• Released Date: 2008-03-04 
Deposition Author(s): Nieman, M.T., Burke, F., Warnock, M., Zhou, Y., Sweigert, J., Chen, A., Ricketts, D., Lucchesi, B.R., Chen, Z., Di Cera, E., Hilfinger, J., Mosberg, H.I., Schmaier, A.H.

Revision History 

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other