5NMV

Crystal structure of 2F22 Fab fragment against TFPI1

• PDB DOI: https://doi.org/10.2210/pdb5NMV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-04-07 Released: 2018-03-28 
• Deposition Author(s): Svensson, L.A., Petersen, H.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Factor Xa and VIIa inhibition by tissue factor pathway inhibitor is prevented by a monoclonal antibody to its Kunitz-1 domain.

Augustsson, C., Svensson, A., Kjaer, B., Chao, T.Y., Wenjuan, X., Krogh, B.O., Breinholt, J., Clausen, J.T., Hilden, I., Petersen, H.H., Petersen, L.C.

(2018) J Thromb Haemost 16: 893-904

• PubMed: 29532595 
• DOI: https://doi.org/10.1111/jth.14000
• Primary Citation of Related Structures:  
  5NMV


• PubMed Abstract: 
  

  Essentials Activated FVII (FVIIa) and FX (FXa) are inhibited by tissue factor pathway inhibitor (TFPI). A monoclonal antibody, mAb2F22, was raised against the N-terminal fragment of TFPI (1-79). mAb2F22 bound exclusively to the K1 domain of TFPI (K _D ∼1 nm) and not to the K2 domain. mAb2F22 interfered with inhibition of both FVIIa and FXa activities and restored clot formation.

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Organizational Affiliation: 

Global Research, Novo Nordisk A/S, Måløv, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.22 kDa 
• Atom Count: 4,403 
• Modelled Residue Count: 496 
• Deposited Residue Count: 521 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	A [auth L]	213	Mus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	B [auth H]	222	Mus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor pathway inhibitor	C [auth K]	86	Homo sapiens	Mutation(s): 0  Gene Names: TFPI, LACI, TFPI1
UniProt & NIH Common Fund Data Resources
Find proteins for P10646 (Homo sapiens) Explore P10646  Go to UniProtKB:  P10646
PHAROS:  P10646 GTEx:  ENSG00000003436

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth L], E [auth L], F [auth H], G [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.01	α = 90
b = 66.66	β = 111.18
c = 106.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Svensson, L.A., Petersen, H.H.

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-05-09
  Changes: Data collection, Database references