1N4X

Structure of scFv 1696 at acidic pH

• PDB DOI: https://doi.org/10.2210/pdb1N4X/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-11-02 Released: 2003-06-10 
• Deposition Author(s): Lescar, J., Brynda, J., Fabry, M., Horejsi, M., Rezacova, P., Sedlacek, J., Bentley, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.256 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

Structure of a single-chain Fv fragment of an antibody that inhibits the HIV-1 and HIV-2 proteases.

Lescar, J., Brynda, J., Fabry, M., Horejsi, M., Rezacova, P., Sedlacek, J., Bentley, G.A.

(2003) Acta Crystallogr D Biol Crystallogr 59: 955-957

• PubMed: 12777823 
• DOI: https://doi.org/10.1107/s0907444903003597
• Primary Citation of Related Structures:  
  1N4X


• PubMed Abstract: 
  

  The monoclonal antibody 1696, which was raised against the HIV-1 protease, inhibits the catalytic activity of the enzyme from both the HIV-1 and HIV-2 strains. The antibody cross-reacts with peptides containing the N-terminus of the enzyme, which is highly conserved between these strains. The crystal structure of a single-chain Fv fragment of 1696 (scFv-1696) in the non-complexed form, solved at 1.7 A resolution, is compared with the previously reported non-complexed Fab-1696 and antigen-bound scFv-1696 structures. Large conformational changes in the third hypervariable region of the heavy chain and differences in relative orientation of the variable domains are observed between the different structures.

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Organizational Affiliation: 

European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.08 kDa 
• Atom Count: 4,188 
• Modelled Residue Count: 465 
• Deposited Residue Count: 466 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin kappa chain variable region	A [auth L], C [auth M]	113	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01631 (Mus musculus) Explore P01631  Go to UniProtKB:  P01631

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin heavy chain variable region	B [auth H], D [auth I]	120	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q921A6 (Mus musculus) Explore Q921A6  Go to UniProtKB:  Q921A6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth H], F [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.256 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.93	α = 90
b = 61.21	β = 90
c = 57.3	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Lescar, J., Brynda, J., Fabry, M., Horejsi, M., Rezacova, P., Sedlacek, J., Bentley, G.A.

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations