1BVK | pdb_00001bvk

HUMANIZED ANTI-LYSOZYME FV COMPLEXED WITH LYSOZYME

• PDB DOI: https://doi.org/10.2210/pdb1BVK/pdb

• Classification: COMPLEX (HUMANIZED ANTIBODY/HYDROLASE)
• Organism(s): Homo sapiens, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-09-16 Released: 1999-02-16 
• Deposition Author(s): Holmes, M.A., Buss, T.N., Foote, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.297 (Depositor) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Conformational correction mechanisms aiding antigen recognition by a humanized antibody.

Holmes, M.A., Buss, T.N., Foote, J.

(1998) J Exp Medicine 187: 479-485

• PubMed: 9463398 
• DOI: https://doi.org/10.1084/jem.187.4.479
• Primary Citation Related Structures: 
  1BVK


• PubMed Abstract: 
  

  The crystal structure of the complex between hen egg lysozyme and the Fv fragment of a humanized antilysozyme antibody was determined to 2.7-A resolution. The structure of the antigen combining site in the complex is nearly identical to that of the complexed form of the parent mouse antibody, D1.3. In contrast, the combining sites of the unliganded mouse and humanized antilysozymes show moderate conformational differences. This disparity suggests that a conformational readjustment process linked to antigen binding reverses adverse conformations in the complementarity determining regions that had been introduced by engineering these segments next to human framework regions in the humanized antibody.

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Organizational Affiliation: 
• Division of Molecular Medicine, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.

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 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.33 kDa 
• Atom Count: 5,488 
• Modeled Residue Count: 706 
• Deposited Residue Count: 708 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HULYS11	A, D	108	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HULYS11	B, E	117	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	C, F	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.297 (Depositor) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.7	α = 90
b = 97.7	β = 90
c = 174.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-16 
Deposition Author(s): Holmes, M.A., Buss, T.N., Foote, J.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary