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.

Macromolecule Content

• Total Structure Weight: 34.60 kDa 
• Atom Count: 2557 
• Residue Count: 288 
• Unique protein chains: 3

1YPG

Thrombin Inhibitor Complex

• DOI: 10.2210/pdb1YPG/pdb

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


• Deposited: 2005-01-31 Released: 2006-01-17 
• Deposition Author(s): Fokkens, J., Obst-Sander, U., Heine, A., Diederich, F., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates

Fokkens, J., Klebe, G.

(2006) Angew Chem Int Ed Engl 45: 985-989

• PubMed: 16374786 
• DOI: 10.1002/anie.200502302
• Primary Citation of Related Structures:  
  1YP9, 1YPG, 1YPE, 1YPK, 1YPJ, 1Y3Y, 1Y3X, 1Y3W, 1Y3V

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	L	27	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
Thrombin heavy chain	H	257	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
Hirudin	I	10	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
UIR	H	(1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE C27 H30 N4 O3 XYMBMAVAMICSMV-FTSNLURZSA-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 %)
UIR	Ki:  10   nM  Binding MOAD
UIR	Ki :  10   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.993	α = 90
b = 71.619	β = 100.6
c = 72.29	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-31 
• Released Date: 2006-01-17 
Deposition Author(s): Fokkens, J., Obst-Sander, U., Heine, A., Diederich, F., Klebe, G.

Revision History 

• Version 1.0: 2006-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2013-03-13
  Changes: Other
• Version 1.5: 2013-11-13
  Changes: Other
• Version 1.6: 2017-10-11
  Changes: Refinement description