1ZTK | pdb_00001ztk

Crystal Structure of the Catalytic Domain of Coagulation Factor XI in Complex with 2-(5-Amino-6-oxo-2-m-tolyl-6H-pyrimidin-1-yl)-N-[4-guanidino-1-(thiazole-2-carbonyl)-butyl]-acetamide

• PDB DOI: https://doi.org/10.2210/pdb1ZTK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2005-05-27 Released: 2006-05-09 
• Deposition Author(s): Nagafuji, P., Jin, L., Rynkiewicz, M., Quinn, J., Bibbins, F., Meyers, H., Babine, R.E., Strickler, J.E., Abdel-Meguid, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.211 (DCC) 

Starting Model: experimental

Literature

Pyrimidinone Inhibitors of a Thrombolytic Protease

Nagafuji, P., Jin, L., Rynkiewicz, M., Quinn, J., Bibbins, F., Meyers, H., Babine, R.E., Strickler, J.E., Abdel-Meguid, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.43 kDa 
• Atom Count: 1,981 
• Modeled Residue Count: 237 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XI	A	238	Homo sapiens	Mutation(s): 4  Gene Names: F11 EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens) Explore P03951  Go to UniProtKB:  P03951
PHAROS:  P03951 GTEx:  ENSG00000088926

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
62A	D [auth A]	2-(5-AMINO-6-OXO-2-M-TOLYL-6H-PYRIMIDIN-1-YL)-N-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL)-BUTYL]-ACETAMIDE C22 H26 N8 O3 S WNJLVFWJWNGWKN-INIZCTEOSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.211 (DCC) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.791	α = 90
b = 121.791	β = 90
c = 121.791	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-09 
Deposition Author(s): Nagafuji, P., Jin, L., Rynkiewicz, M., Quinn, J., Bibbins, F., Meyers, H., Babine, R.E., Strickler, J.E., Abdel-Meguid, S.S.

Revision History  

• Version 1.0: 2006-05-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary