PDBsum entry 1xgp

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protein Protein-protein interface(s) links
Immune system PDB id
Protein chains
215 a.a.
210 a.a. *
129 a.a. *
Waters ×431
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Structure for antibody hyhel-63 y33a mutant complexed with hen egg lysozyme
Structure: Antibody kappa light chain. Chain: a. Engineered: yes. Antibody kappa heavy chain. Chain: b. Engineered: yes. Mutation: yes. LysozymE C. Chain: c.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Gallus gallus. Chicken. Organism_taxid: 9031. Other_details: hen egg white
Biol. unit: Trimer (from PQS)
2.10Å     R-factor:   0.215     R-free:   0.271
Authors: Y.Li,R.A.Mariuzza
Key ref:
Y.Li et al. (2005). Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces. Structure, 13, 297-307. PubMed id: 15698573 DOI: 10.1016/j.str.2004.12.012
17-Sep-04     Release date:   06-Sep-05    
Go to PROCHECK summary

Protein chain
No UniProt id for this chain
Struc: 215 a.a.
Protein chain
No UniProt id for this chain
Struc: 210 a.a.
Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C
147 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain C: E.C.  - 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   3 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     6 terms  


DOI no: 10.1016/j.str.2004.12.012 Structure 13:297-307 (2005)
PubMed id: 15698573  
Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces.
Y.Li, Y.Huang, C.P.Swaminathan, S.J.Smith-Gill, R.A.Mariuzza.
Hydrophobic interactions are essential for stabilizing protein-protein complexes, whose interfaces generally consist of a central cluster of hot spot residues surrounded by less important peripheral residues. According to the O-ring hypothesis, a condition for high affinity binding is solvent exclusion from interacting residues. This hypothesis predicts that the hydrophobicity at the center is significantly greater than at the periphery, which we estimated at 21 cal mol(-1) A(-2). To measure the hydrophobicity at the center, structures of an antigen-antibody complex where a buried phenylalanine was replaced by smaller hydrophobic residues were determined. By correlating structural changes with binding free energies, we estimate the hydrophobicity at this central site to be 46 cal mol(-1) A(-2), twice that at the periphery. This context dependence of the hydrophobic effect explains the clustering of hot spots at interface centers and has implications for hot spot prediction and the design of small molecule inhibitors.
  Selected figure(s)  
Figure 5.
Figure 5. Schematic Representations of H63-HEL Reference and Mutant Complexes in the Region of Residue V[H]33
Van der Waals contacts between residue V[H]33 and HEL are represented as thick dotted lines; contacts between this residue and adjacent antibody residues are drawn as thin dotted lines. (A) V[H]Phe33-HEL. (B) V[H]Leu33-HEL. (C) V[H]Ile33-HEL. (D) V[H]Val33-HEL. (E) V[H]Ala33-HEL. No buried water molecules are observed at the mutation site in any of the interfaces. The hydrogen bonding network in the vicinity of residue V[H]33 (not shown), or elsewhere in the interface is unaffected by the mutations.
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 297-307) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20865533 U.D.Ramirez, F.Myachina, L.Stith, and E.K.Jaffe (2010).
Docking to large allosteric binding sites on protein surfaces.
  Adv Exp Med Biol, 680, 481-488.  
19479323 M.Guharoy, and P.Chakrabarti (2009).
Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes.
  J Comput Aided Mol Des, 23, 645-654.  
17166830 M.Shiroishi, K.Tsumoto, Y.Tanaka, A.Yokota, T.Nakanishi, H.Kondo, and I.Kumagai (2007).
Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL.
  J Biol Chem, 282, 6783-6791.
PDB codes: 2dqc 2dqd 2dqe 2dqf 2dqg 2dqh 2dqi 2dqj
17145365 R.J.Duquesnoy (2006).
A structurally based approach to determine HLA compatibility at the humoral immune level.
  Hum Immunol, 67, 847-862.  
16336694 K.V.Brinda, and S.Vishveshwara (2005).
Oligomeric protein structure networks: insights into protein-protein interactions.
  BMC Bioinformatics, 6, 296.  
16338406 S.Cho, C.P.Swaminathan, J.Yang, M.C.Kerzic, R.Guan, M.C.Kieke, D.M.Kranz, R.A.Mariuzza, and E.J.Sundberg (2005).
Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.
  Structure, 13, 1775-1787.  
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