PDBsum entry 1a2y

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protein ligands Protein-protein interface(s) links
Complex (immunoglobulin/hydrolase) PDB id
Protein chains
107 a.a. *
116 a.a. *
129 a.a. *
Waters ×485
* Residue conservation analysis
PDB id:
Name: Complex (immunoglobulin/hydrolase)
Title: Hen egg white lysozyme, d18a mutant, in complex with mouse monoclonal antibody d1.3
Structure: Igg1-kappa d1.3 fv (light chain). Chain: a. Engineered: yes. Igg1-kappa d1.3 fv (heavy chain). Chain: b. Engineered: yes. Lysozyme. Chain: c. Engineered: yes.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Organ: egg. Expressed in: escherichia coli. Expression_system_taxid: 562. Gallus gallus. Chicken. Organism_taxid: 9031.
Biol. unit: Trimer (from PQS)
1.50Å     R-factor:   0.203     R-free:   0.251
Authors: D.Tsuchiya,R.A.Mariuzza
Key ref:
W.Dall'Acqua et al. (1998). A mutational analysis of binding interactions in an antigen-antibody protein-protein complex. Biochemistry, 37, 7981-7991. PubMed id: 9609690 DOI: 10.1021/bi980148j
13-Jan-98     Release date:   29-Apr-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P01635  (KV5A3_MOUSE) -  Ig kappa chain V-V region K2 (Fragment)
115 a.a.
107 a.a.*
Protein chain
Pfam   ArchSchema ?
P01820  (HVM44_MOUSE) -  Ig heavy chain V region PJ14
115 a.a.
116 a.a.*
Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C
147 a.a.
129 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 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     7 terms  


DOI no: 10.1021/bi980148j Biochemistry 37:7981-7991 (1998)
PubMed id: 9609690  
A mutational analysis of binding interactions in an antigen-antibody protein-protein complex.
W.Dall'Acqua, E.R.Goldman, W.Lin, C.Teng, D.Tsuchiya, H.Li, X.Ysern, B.C.Braden, Y.Li, S.J.Smith-Gill, R.A.Mariuzza.
Alanine scanning mutagenesis, double mutant cycles, and X-ray crystallography were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Twelve out of the 13 nonglycine contact residues on HEL, as determined by the high-resolution crystal structure of the D1.3-HEL complex, were individually truncated to alanine. Only four positions showed a DeltaDeltaG (DeltaGmutant - DeltaGwild-type) of greater than 1.0 kcal/mol, with HEL residue Gln121 proving the most critical for binding (DeltaDeltaG = 2.9 kcal/mol). These residues form a contiguous patch at the periphery of the epitope recognized by D1.3. To understand how potentially disruptive mutations in the antigen are accommodated in the D1.3-HEL interface, we determined the crystal structure to 1.5 A resolution of the complex between D1.3 and HEL mutant Asp18 --> Ala. This mutation results in a DeltaDeltaG of only 0.3 kcal/mol, despite the loss of a hydrogen bond and seven van der Waals contacts to the Asp18 side chain. The crystal structure reveals that three additional water molecules are stably incorporated in the antigen-antibody interface at the site of the mutation. These waters help fill the cavity created by the mutation and form part of a rearranged solvent network linking the two proteins. To further dissect the energetics of specific interactions in the D1.3-HEL interface, double mutant cycles were carried out to measure the coupling of 14 amino acid pairs, 10 of which are in direct contact in the crystal structure. The highest coupling energies, 2.7 and 2.0 kcal/mol, were measured between HEL residue Gln121 and D1.3 residues VLTrp92 and VLTyr32, respectively. The interaction between Gln121 and VLTrp92 consists of three van der Waals contacts, while the interaction of Gln121 with VLTyr32 is mediated by a hydrogen bond. Surprisingly, however, most cycles between interface residues in direct contact in the crystal structure showed no significant coupling. In particular, a number of hydrogen-bonded residue pairs were found to make no net contribution to complex stabilization. We attribute these results to accessibility of the mutation sites to water, such that the mutated residues exchange their interaction with each other to interact with water. This implies that the strength of the protein-protein hydrogen bonds in these particular cases is comparable to that of the protein-water hydrogen bonds they replace. Thus, the simple fact that two residues are in direct contact in a protein-protein interface cannot be taken as evidence that there necessarily exists a productive interaction between them. Rather, the majority of such contacts may be energetically neutral, as in the D1.3-HEL complex.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21269500 A.K.Füzéry, J.J.Oh, D.T.Ta, L.E.Vickery, and J.L.Markley (2011).
Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complex.
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Phylogenetic and structural analysis of the HbA (alphaA/betaA) and HbD (alphaD/betaA) hemoglobin genes in two high-altitude waterfowl from the Himalayas and the Andes: Bar-headed goose (Anser indicus) and Andean goose (Chloephaga melanoptera).
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Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes.
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Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl.
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Incorporating receptor flexibility in the molecular design of protein interfaces.
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Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations.
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17085574 L.V.Wray, and S.H.Fisher (2007).
Functional analysis of the carboxy-terminal region of Bacillus subtilis TnrA, a MerR family protein.
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17252586 M.J.Bobeck, and G.D.Glick (2007).
Role of conformational dynamics in sequence-specific autoantibody*ssDNA recognition.
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17652781 N.Sinha, Y.Li, C.A.Lipschultz, and S.J.Smith-Gill (2007).
Understanding antibody-antigen associations by molecular dynamics simulations: detection of important intra- and inter-molecular salt bridges.
  Cell Biochem Biophys, 47, 361-375.  
17418361 R.Pantophlet, R.O.Aguilar-Sino, T.Wrin, L.A.Cavacini, and D.R.Burton (2007).
Analysis of the neutralization breadth of the anti-V3 antibody F425-B4e8 and re-assessment of its epitope fine specificity by scanning mutagenesis.
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17517649 S.W.Chi, C.Y.Maeng, S.J.Kim, M.S.Oh, C.J.Ryu, S.J.Kim, K.H.Han, H.J.Hong, and S.E.Ryu (2007).
Broadly neutralizing anti-hepatitis B virus antibody reveals a complementarity determining region H3 lid-opening mechanism.
  Proc Natl Acad Sci U S A, 104, 9230-9235.
PDB codes: 2eh7 2eh8
17568777 T.Tanaka, R.L.Williams, and T.H.Rabbitts (2007).
Tumour prevention by a single antibody domain targeting the interaction of signal transduction proteins with RAS.
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PDB code: 2uzi
17242738 Z.Li, and T.Lazaridis (2007).
Water at biomolecular binding interfaces.
  Phys Chem Chem Phys, 9, 573-581.  
16861345 D.W.Bougie, P.R.Wilker, and R.H.Aster (2006).
Patients with quinine-induced immune thrombocytopenia have both "drug-dependent" and "drug-specific" antibodies.
  Blood, 108, 922-927.  
16881059 J.C.Almagro, V.Quintero-Hernández, M.Ortiz-León, A.Velandia, S.L.Smith, and B.Becerril (2006).
Design and validation of a synthetic VH repertoire with tailored diversity for protein recognition.
  J Mol Recognit, 19, 413-422.  
16950393 J.Sohn, and J.Rudolph (2006).
The energetic network of hotspot residues between Cdc25B phosphatase and its protein substrate.
  J Mol Biol, 362, 1060-1071.  
17145365 R.J.Duquesnoy (2006).
A structurally based approach to determine HLA compatibility at the humoral immune level.
  Hum Immunol, 67, 847-862.  
16864573 S.J.Fleishman, A.D.Sabag, E.Ophir, K.B.Avraham, and N.Ben-Tal (2006).
The structural context of disease-causing mutations in gap junctions.
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15856483 F.Rodier, R.P.Bahadur, P.Chakrabarti, and J.Janin (2005).
Hydration of protein-protein interfaces.
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15858274 G.H.Cohen, E.W.Silverton, E.A.Padlan, F.Dyda, J.A.Wibbenmeyer, R.C.Willson, and D.R.Davies (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.
PDB code: 1yqv
16196088 M.Fuentes, C.Mateo, B.C.Pessela, J.M.Guisán, and R.Fernandez-Lafuente (2005).
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15459238 M.O.Popa, A.K.Alekov, S.Bail, F.Lehmann-Horn, and H.Lerche (2004).
Cooperative effect of S4-S5 loops in domains D3 and D4 on fast inactivation of the Na+ channel.
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15382230 S.Liang, J.Zhang, S.Zhang, and H.Guo (2004).
Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores.
  Proteins, 57, 548-557.  
14962388 Y.Zhao, Z.Li, S.J.Drozd, Y.Guo, W.Mourad, and H.Li (2004).
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  Structure, 12, 277-288.
PDB code: 1r5i
14573859 B.W.Bailey, B.Mumey, P.A.Hargrave, A.Arendt, O.P.Ernst, K.P.Hofmann, P.R.Callis, J.B.Burritt, A.J.Jesaitis, and E.A.Dratz (2003).
Constraints on the conformation of the cytoplasmic face of dark-adapted and light-excited rhodopsin inferred from antirhodopsin antibody imprints.
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Complete analysis of the B-cell response to a protein antigen, from in vivo germinal centre formation to 3-D modelling of affinity maturation.
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  Trends Immunol, 24, 429-437.  
12719580 M.B.Zwick, P.W.Parren, E.O.Saphire, S.Church, M.Wang, J.K.Scott, P.E.Dawson, I.A.Wilson, and D.R.Burton (2003).
Molecular features of the broadly neutralizing immunoglobulin G1 b12 required for recognition of human immunodeficiency virus type 1 gp120.
  J Virol, 77, 5863-5876.  
12761222 M.del Alamo, J.L.Neira, and M.G.Mateu (2003).
Thermodynamic dissection of a low affinity protein-protein interface involved in human immunodeficiency virus assembly.
  J Biol Chem, 278, 27923-27929.  
12740607 Y.Li, H.Li, F.Yang, S.J.Smith-Gill, and R.A.Mariuzza (2003).
X-ray snapshots of the maturation of an antibody response to a protein antigen.
  Nat Struct Biol, 10, 482-488.
PDB codes: 1ndg 1ndm
12501160 A.V.Veselovsky, Y.D.Ivanov, A.S.Ivanov, A.I.Archakov, P.Lewi, and P.Janssen (2002).
Protein-protein interactions: mechanisms and modification by drugs.
  J Mol Recognit, 15, 405-422.  
12447904 D.Altschuh (2002).
Cyclosporin A as a model antigen: immunochemical and structural studies.
  J Mol Recognit, 15, 277-285.  
12048184 E.De Genst, D.Areskoug, K.Decanniere, S.Muyldermans, and K.Andersson (2002).
Kinetic and affinity predictions of a protein-protein interaction using multivariate experimental design.
  J Biol Chem, 277, 29897-29907.  
11994422 J.G.Luz, M.Huang, K.C.Garcia, M.G.Rudolph, V.Apostolopoulos, L.Teyton, and I.A.Wilson (2002).
Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.
  J Exp Med, 195, 1175-1186.
PDB codes: 1jtr 1leg 1lek 1mwa
12414693 M.A.Eriksson, and B.Roux (2002).
Modeling the structure of agitoxin in complex with the Shaker K+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles.
  Biophys J, 83, 2595-2609.  
12496069 N.Sinha, S.Mohan, C.A.Lipschultz, and S.J.Smith-Gill (2002).
Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity.
  Biophys J, 83, 2946-2968.  
11698684 L.C.Roisman, J.Piehler, J.Y.Trosset, H.A.Scheraga, and G.Schreiber (2001).
Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking.
  Proc Natl Acad Sci U S A, 98, 13231-13236.  
11290333 M.G.Rudolph, J.A.Speir, A.Brunmark, N.Mattsson, M.R.Jackson, P.A.Peterson, L.Teyton, and I.A.Wilson (2001).
The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity.
  Immunity, 14, 231-242.
PDB codes: 1fzj 1fzk 1fzm 1fzo
11375496 X.Z.Liu, S.L.Li, H.Jing, Y.H.Liang, Z.Q.Hua, and G.Y.Lu (2001).
Avian haemoglobins and structural basis of high affinity for oxygen: structure of bar-headed goose aquomet haemoglobin.
  Acta Crystallogr D Biol Crystallogr, 57, 775-783.
PDB code: 1c40
11717498 Y.H.Liang, X.Z.Liu, S.H.Liu, and G.Y.Lu (2001).
The structure of greylag goose oxy haemoglobin: the roles of four mutations compared with bar-headed goose haemoglobin.
  Acta Crystallogr D Biol Crystallogr, 57, 1850-1856.
PDB code: 1faw
10899782 D.Fleury, R.S.Daniels, J.J.Skehel, M.Knossow, and T.Bizebard (2000).
Structural evidence for recognition of a single epitope by two distinct antibodies.
  Proteins, 40, 572-578.
PDB code: 1eo8
11112523 E.J.Sundberg, M.Urrutia, B.C.Braden, J.Isern, D.Tsuchiya, B.A.Fields, E.L.Malchiodi, J.Tormo, F.P.Schwarz, and R.A.Mariuzza (2000).
Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.
  Biochemistry, 39, 15375-15387.
PDB codes: 1g7h 1g7i 1g7j 1g7l 1g7m
11123892 S.Lang, J.Xu, F.Stuart, R.M.Thomas, J.W.Vrijbloed, and J.A.Robinson (2000).
Analysis of antibody A6 binding to the extracellular interferon gamma receptor alpha-chain by alanine-scanning mutagenesis and random mutagenesis with phage display.
  Biochemistry, 39, 15674-15685.  
10828942 Y.Li, H.Li, S.J.Smith-Gill, and R.A.Mariuzza (2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
  Biochemistry, 39, 6296-6309.
PDB codes: 1dqj 1dqm 1dqq
10451557 B.Selisko, A.F.Licea, B.Becerril, F.Zamudio, L.D.Possani, and E.Horjales (1999).
Antibody BCF2 against scorpion toxin Cn2 from Centuroides noxius Hoffmann: primary structure and three-dimensional model as free Fv fragment and complexed with its antigen.
  Proteins, 37, 130-143.  
10531324 C.P.Swaminathan, A.Nandi, S.S.Visweswariah, and A.Surolia (1999).
Thermodynamic analyses reveal role of water release in epitope recognition by a monoclonal antibody against the human guanylyl cyclase C receptor.
  J Biol Chem, 274, 31272-31278.  
10611648 D.G.Myszka (1999).
Survey of the 1998 optical biosensor literature.
  J Mol Recognit, 12, 390-408.  
10358765 H.Li, A.Llera, E.L.Malchiodi, and R.A.Mariuzza (1999).
The structural basis of T cell activation by superantigens.
  Annu Rev Immunol, 17, 435-466.  
10647173 J.Janin (1999).
Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition.
  Structure, 7, R277-R279.  
  10338006 J.Pons, A.Rajpal, and J.F.Kirsch (1999).
Energetic analysis of an antigen/antibody interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/lysozyme interaction.
  Protein Sci, 8, 958-968.  
10413475 T.A.Isenbarger, and M.P.Krebs (1999).
Role of helix-helix interactions in assembly of the bacteriorhodopsin lattice.
  Biochemistry, 38, 9023-9030.  
9881971 H.Li, A.Llera, D.Tsuchiya, L.Leder, X.Ysern, P.M.Schlievert, K.Karjalainen, and R.A.Mariuzza (1998).
Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B.
  Immunity, 9, 807-816.
PDB code: 1sbb
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.