Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.68 kDa 
• Atom Count: 4842 
• Modelled Residue Count: 604 
• Deposited Residue Count: 615 
• Unique protein chains: 2

5I25

human recombinant coagulation FXI in complex with a peptide derived from human high molecular weight kininogen (HKP)

• PDB DOI: 10.2210/pdb5I25/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, synthetic construct
• Mutation(s): No 


• Deposited: 2016-02-08 Released: 2016-04-06 
• Deposition Author(s): Hall, G.A.F., Wong, S.S., Emsley, J.
• Funding Organization(s): British Heart Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.288 
• R-Value Work: 0.226 
• R-Value Observed: 0.232 

Literature

A novel DFP tripeptide motif interacts with the coagulation factor XI apple 2 domain.

Wong, S.S., stergaard, S., Hall, G., Li, C., Williams, P.M., Stennicke, H., Emsley, J.

(2016) Blood 127: 2915-2923

• PubMed: 27006387 
• DOI: 10.1182/blood-2015-10-676122
• Primary Citation of Related Structures:  
  5EOD, 5EOK, 5I25


• PubMed Abstract: 
  

Factor XI (FXI) is the zymogen of FXIa, which cleaves FIX in the intrinsic pathway of coagulation. FXI is known to exist as a dimer and interacts with multiple proteins via its 4 apple domains in the "saucer section" of the enzyme; however, to date, no complex crystal structure has been described. To investigate protein interactions of FXI, a large random peptide library consisting of 10(6) to 10(7) peptides was screened for FXI binding, which identified a series of FXI binding motifs containing the signature Asp-Phe-Pro (DFP) tripeptide. Motifs containing this core tripeptide were found in diverse proteins, including the known ligand high-molecular-weight kininogen (HK), as well as the extracellular matrix proteins laminin and collagen V. To define the binding site on FXI, we determined the crystal structure of FXI in complex with the HK-derived peptide NPISDFPDT. This revealed the location of the DFP peptide bound to the FXI apple 2 domain, and central to the interaction, the DFP phenylalanine side-chain inserts into a major hydrophobic pocket in the apple 2 domain and the isoleucine occupies a flanking minor pocket. Two further structures of FXI in complex with the laminin-derived peptide EFPDFP and a DFP peptide from the random screen demonstrated binding in the same pocket, although in a slightly different conformation, thus revealing some flexibility in the molecular interactions of the FXI apple 2 domain.

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Organizational Affiliation: 

Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom; and.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XI	A	607	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ASN-PRO-ILE-SER-ASP-PHE-PRO-ASP	B	8	Homo sapiens	Mutation(s): 0  Gene Names: KNG1, BDK, KNG
UniProt & NIH Common Fund Data Resources
Find proteins for P01042 (Homo sapiens) Explore P01042  Go to UniProtKB:  P01042
PHAROS:  P01042 GTEx:  ENSG00000113889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.288 
• R-Value Work: 0.226 
• R-Value Observed: 0.232 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.59	α = 90
b = 80.59	β = 90
c = 251.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-02-08 
• Released Date: 2016-04-06 
Deposition Author(s): Hall, G.A.F., Wong, S.S., Emsley, J.

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Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	--

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2016-06-22
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary