2ZDV

Exploring Thrombin S1 pocket

• PDB DOI: https://doi.org/10.2210/pdb2ZDV/pdb

• Classification: Blood Clotting/Hydrolase Inhibitor
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2007-11-29 Released: 2008-10-28 
• Deposition Author(s): Baum, B., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.243 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Exploring Thrombin S1 pocket

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 35.81 kDa 
• Atom Count: 2,602 
• Modelled Residue Count: 289 
• Deposited Residue Count: 306 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin Light Chain	A [auth L]	36	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin Heavy Chain	B [auth H]	259	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-1	C [auth I]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050  Go to UniProtKB:  P01050

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
37U	G [auth H]	D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide C21 H24 F N3 O2 JGZSVYZIJHGHMA-MOPGFXCFSA-N
PO4	F [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	D [auth H], E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000602 (37U)	G [auth H]	D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide	Peptide-like / Thrombin inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.243 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.5	α = 90
b = 71.4	β = 100.6
c = 72.8	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Baum, B., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2008-10-28
  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
• Version 1.3: 2016-05-25
  Changes: Source and taxonomy
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection
• Version 1.7: 2024-10-30
  Changes: Structure summary