2IFF | pdb_00002iff

STRUCTURE OF AN ANTIBODY-LYSOZYME COMPLEX: EFFECT OF A CONSERVATIVE MUTATION

• PDB DOI: https://doi.org/10.2210/pdb2IFF/pdb

• Classification: IMMUNOGLOBULIN/HYDROLASE(O-GLYCOSYL)
• Organism(s): Mus musculus, Gallus gallus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1994-02-03 Released: 1994-05-31 
• Deposition Author(s): Chacko, S., Davies, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Work: 
  0.160 (DCC) 

Literature

Structure of an antibody-lysozyme complex unexpected effect of conservative mutation.

Chacko, S., Silverton, E., Kam-Morgan, L., Smith-Gill, S., Cohen, G., Davies, D.

(1995) J Mol Biology 245: 261-274

• PubMed: 7531245 
• DOI: https://doi.org/10.1006/jmbi.1994.0022
• Primary Citation Related Structures: 
  2IFF


• PubMed Abstract: 
  

  The structure of the complex between the Fab HyHEL-5 and chicken lysozyme revealed a large interface region containing 23 lysozyme and 28 Fab residues. Arg68 of the lysozyme is centrally placed in this interface and theoretical studies together with binding assays of this Fab to different avian lysozymes have previously shown that this arginine residue is an important contributor to the binding. The Arg68-->Lys mutant binds 10(3) times less well to the HyHEL-5 Fab. We have examined the refined crystal structure of the complex of this mutant lysozyme with the Fab. No global changes occur, but there is an introduction of a new water molecule into the interface that mediates the hydrogen bonding interactions between the lysine and residues on the Fab. These data are compared with the effects of similar changes on the inhibition of serine proteases such as trypsin where the energetic effects of this substitution are small.

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Organizational Affiliation: 
• NIDDK, National Institutes of Health, Bethesda, MD.

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.

Macromolecule Content 

• Total Structure Weight: 60.61 kDa 
• Atom Count: 4,325 
• Modeled Residue Count: 555 
• Deposited Residue Count: 556 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG1 HYHEL-5 FAB (LIGHT CHAIN)	A [auth L]	212	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG1 HYHEL-5 FAB (HEAVY CHAIN)	B [auth H]	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEN EGG WHITE LYSOZYME	C [auth Y]	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: 2.65 Å
• R-Value Work:  0.160 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.8	α = 90
b = 74.8	β = 101.8
c = 79	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-05-31 
Deposition Author(s): Chacko, S., Davies, D.R.

Revision History  

• Version 1.0: 1994-05-31
  Type: Initial release
  
• Version 1.1: 2008-03-10
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-08-10
  Changes: Structure summary
• Version 1.4: 2024-06-05
  Changes: Data collection, Database references, Other
• Version 1.5: 2024-11-13
  Changes: Structure summary