1ZTJ | pdb_00001ztj

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

• PDB DOI: https://doi.org/10.2210/pdb1ZTJ/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: 2.05 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (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: 27.53 kDa 
• Atom Count: 2,151 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
632	E [auth A]	2-(5-BENZYLAMINO-2-METHYLSULFANYL-6-OXO-6H-PYRIMIDIN-1-YL)-N-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL)-BUTYL]-ACETAMIDE C23 H28 N8 O3 S2 NSVPIISNZVMCCY-INIZCTEOSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BCT	D [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.674	α = 90
b = 120.674	β = 90
c = 120.674	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: 2024-11-06
  Changes: Structure summary