Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 35856.82 
• Atom Count: 2326 
• Residue Count: 307 
• Unique protein chains: 3

2ZHW

Exploring thrombin S3 pocket

• DOI: 10.2210/pdb2ZHW/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Hirudo medicinalis, Homo sapiens


• Deposited: 2008-02-08 Released: 2009-02-10 
• Deposition Author(s): Brandt, T., Baum, B., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.292 
• R-Value Work: 0.188 

Literature

Exploring thrombin S3 pocket

Brandt, T., Baum, B., Hangauer, D., Heine, A., Klebe, G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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: 2
Molecule	Chains	Sequence Length	Organism	Details
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: 3
Molecule	Chains	Sequence Length	Organism	Details
Hirudin variant-2	I	12	Hirudo medicinalis	Mutation(s): 0
Find proteins for P09945 (Hirudo medicinalis) Go to UniProtKB:  P09945

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
12U	H	N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[2-(cycloheptylamino)ethanoyl]pyrrolidine-2-carboxamide C22 H33 N5 O2 BYTJPDBCLWUEBU-IBGZPJMESA-N
NA	H	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000588 (12U)	H	N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide	Peptide-like / Thrombin inhibitor		--

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.292 
• R-Value Work: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 68.900	α = 90.00
b = 71.500	β = 99.10
c = 71.300	γ = 90.00

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-08 
• Released Date: 2009-02-10 
• Deposition Author(s): Brandt, T., Baum, B., Heine, A., Klebe, G.

Revision History 

• Version 1.0: 2009-02-10
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Type: Other
• Version 1.3: 2016-05-25
  Type: Source and taxonomy