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PDBsum entry 1yqv

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protein Protein-protein interface(s) links
Immune system PDB id
1yqv
Jmol
Contents
Protein chains
211 a.a. *
215 a.a. *
129 a.a. *
Waters ×619
* Residue conservation analysis
PDB id:
1yqv
Name: Immune system
Title: The crystal structure of the antibody fab hyhel5 complex with lysozyme at 1.7a resolution
Structure: Hyhel-5 antibody light chain. Chain: l. Fragment: ig G1 fab fragment (hy/hel-5). Hyhel-5 antibody heavy chain. Chain: h. Fragment: ig G1 fab fragment (hy/hel-5). Hen egg white lysozyme. Chain: y. Synonym: 1,4-beta-n-acetylmuramidasE C, allergen gal d 4,
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb-c. Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: egg white
Biol. unit: Trimer (from PQS)
Resolution:
1.70Å     R-factor:   0.195     R-free:   0.234
Authors: G.H.Cohen,E.W.Silverton,E.A.Padlan,F.Dyda,J.A.Wibbenmeyer, R.C.Wilson,D.R.Davies
Key ref:
G.H.Cohen et al. (2005). Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry. Acta Crystallogr D Biol Crystallogr, 61, 628-633. PubMed id: 15858274 DOI: 10.1107/S0907444905007870
Date:
02-Feb-05     Release date:   26-Apr-05    
Supersedes: 3hfl
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 211 a.a.
Protein chain
No UniProt id for this chain
Struc: 215 a.a.
Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C
Seq:
Struc:
147 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain Y: E.C.3.2.1.17  - Lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1107/S0907444905007870 Acta Crystallogr D Biol Crystallogr 61:628-633 (2005)
PubMed id: 15858274  
 
 
Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.
G.H.Cohen, E.W.Silverton, E.A.Padlan, F.Dyda, J.A.Wibbenmeyer, R.C.Willson, D.R.Davies.
 
  ABSTRACT  
 
The structure of the complex between hen egg-white lysozyme and the Fab HyHEL-5 at 2.7 A resolution has previously been reported [Cohen et al. (1996), Acta Cryst. D52, 315-326]. With the availability of recombinant Fab, the X-ray structure of the complex has been re-evaluated at 1.7 A resolution. The refined structure has yielded a detailed picture of the Fab-lysozyme interface, showing the high complementarity of the protein surfaces as well as several water molecules within the interface that complete the good fit. The model of the full complex has improved significantly, yielding an R(work) of 19.5%. With this model, the structural results can be compared with the results of isothermal titration calorimetry. An attempt has been made to estimate the changes in bound waters that accompany complex formation and the difficulties inherent in using the crystal structures to provide the information necessary to make this calculation are discussed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Detailed view of the interactions between seven residues involved in the contacts between the bound lysozyme and the HyHEL-5 antibody. Two residues from lysozyme are shown with blue bonds, two residues from the antibody light chain are shown with yellow bonds and three residues from the heavy chain are shown with green bonds. Hydrogen bonding is shown with thin black bonds. The electron density from a 2F[o] - F[c] map is contoured at 1.8 [sigma] . The diagram was prepared with Ribbons v.3.12 (Carson, 1997 [Carson, M. (1997). Methods Enzymol. 277, 493-505.]-[bluearr.gif] ).
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 628-633) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19767317 C.L.Brooks, R.J.Blackler, G.Sixta, P.Kosma, S.Müller-Loennies, L.Brade, T.Hirama, C.R.MacKenzie, H.Brade, and S.V.Evans (2010).
The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.
  Glycobiology, 20, 138-147.
PDB codes: 3ijh 3ijs 3ijy 3ikc
20969768 I.Amela, P.Delicado, A.Gómez, S.Bonàs, E.Querol, and J.Cedano (2010).
DockAnalyse: an application for the analysis of protein-protein interactions.
  BMC Struct Biol, 10, 37.  
19553661 M.A.Argiriadi, T.Xiang, C.Wu, T.Ghayur, and D.W.Borhani (2009).
Unusual water-mediated antigenic recognition of the proinflammatory cytokine interleukin-18.
  J Biol Chem, 284, 24478-24489.
PDB codes: 2vxt 2vxu 2vxv
19883097 M.Długosz, J.M.Antosiewicz, and J.Trylska (2009).
pH-dependent association of proteins. The test case of monoclonal antibody HyHEL-5 and its antigen hen egg white lysozyme.
  J Phys Chem B, 113, 15662-15669.  
18383102 K.Kourentzi, M.Srinivasan, S.J.Smith-Gill, and R.C.Willson (2008).
Conformational flexibility and kinetic complexity in antibody-antigen interactions.
  J Mol Recognit, 21, 114-121.  
17006876 A.Ababou, and J.E.Ladbury (2007).
Survey of the year 2005: literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 20, 4.  
17445828 E.O.Saphire, M.Montero, A.Menendez, N.E.van Houten, M.B.Irving, R.Pantophlet, M.B.Zwick, P.W.Parren, D.R.Burton, J.K.Scott, and I.A.Wilson (2007).
Structure of a high-affinity "mimotope" peptide bound to HIV-1-neutralizing antibody b12 explains its inability to elicit gp120 cross-reactive antibodies.
  J Mol Biol, 369, 696-709.  
17471455 H.H.Bui, A.J.Schiewe, and I.S.Haworth (2007).
WATGEN: an algorithm for modeling water networks at protein-protein interfaces.
  J Comput Chem, 28, 2241-2251.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.