Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.20 kDa 
• Atom Count: 2221 
• Modelled Residue Count: 237 
• Deposited Residue Count: 238 
• Unique protein chains: 1

1ZHM

Crystal Structure of the Catalytic Domain of the Coagulation Factor XIa in Complex with Benzamidine (S434A-T475A-K437 Mutant)

• PDB DOI: 10.2210/pdb1ZHM/pdb

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


• Deposited: 2005-04-26 Released: 2005-09-20 
• Deposition Author(s): Jin, L., Pandey, P., Babine, R.E., Weaver, D.T., Abdel-Meguid, S.S., Strickler, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.191 
• R-Value Work: 0.170 

Literature

Mutation of surface residues to promote crystallization of activated factor XI as a complex with benzamidine: an essential step for the iterative structure-based design of factor XI inhibitors.

Jin, L., Pandey, P., Babine, R.E., Weaver, D.T., Abdel-Meguid, S.S., Strickler, J.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1418-1425

• PubMed: 16204896 
• DOI: 10.1107/S0907444905024340
• Primary Citation of Related Structures:  
  1ZHM, 1ZHP, 1ZHR


• PubMed Abstract: 
  

Activated factor XI (FXIa) is a key enzyme in the amplification phase of the blood-coagulation cascade. Thus, a selective FXIa inhibitor may have lesser bleeding liabilities and provide a safe alternative for antithrombosis therapy to available drugs on the market. In a previous report, the crystal structures of the catalytic domain of FXIa (rhFXI(370-607)) in complex with various ecotin mutants have been described. However, ecotin forms a matrix-like interaction with rhFXI(370-607) and is impossible to displace with small-molecule inhibitors; ecotin crystals are therefore not suitable for iterative structure-based ligand design. In addition, rhFXI(370-607) did not crystallize in the presence of small-molecule ligands. In order to obtain the crystal structure of rhFXI(370-607) with a weak small-molecule ligand, namely benzamidine, several rounds of surface-residue mutation were implemented to promote crystal formation of rhFXI(370-607). A quadruple mutant of rhFXI(370-607) (rhFXI(370-607)-S434A,T475A,C482S,K437A) readily crystallized in the presence of benzamidine. The benzamidine in the preformed crystals was easily exchanged with other FXIa small-molecule inhibitors. These crystals have facilitated the structure-based design of small-molecule FXIa inhibitors.

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Organizational Affiliation: 

Daiichi Asubio Medical Research Laboratories LLC, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
coagulation factor XI	A	238	Homo sapiens	Mutation(s): 3  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	C [auth A]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
BEN	B [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.191 
• R-Value Work: 0.170 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.052	α = 90
b = 120.052	β = 90
c = 120.052	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-26 
• Released Date: 2005-09-20 
Deposition Author(s): Jin, L., Pandey, P., Babine, R.E., Weaver, D.T., Abdel-Meguid, S.S., Strickler, J.E.

Revision History  

• Version 1.0: 2005-09-20
  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