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PDBsum entry 1dkk

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protein ligands Protein-protein interface(s) links
Hydrolase (o-glycosyl) PDB id
1dkk
Jmol
Contents
Protein chains
129 a.a. *
Ligands
NO3 ×4
Waters ×154
* Residue conservation analysis
PDB id:
1dkk
Name: Hydrolase (o-glycosyl)
Title: Bobwhite quail lysozyme with nitrate
Structure: Lysozyme. Chain: a, b. Ec: 3.2.1.17
Source: Colinus virginianus. Northern bobwhite. Organism_taxid: 9014. Cell: egg
Resolution:
1.90Å     R-factor:   0.157    
Authors: P.D.Jeffrey,S.Sheriff
Key ref: S.Chacko et al. (1996). Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment. Proteins, 26, 55-65. PubMed id: 8880929
Date:
10-Jan-96     Release date:   11-Jul-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00700  (LYSC_COLVI) -  Lysozyme C
Seq:
Struc:
129 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
Proteins 26:55-65 (1996)
PubMed id: 8880929  
 
 
Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment.
S.Chacko, E.W.Silverton, S.J.Smith-Gill, D.R.Davies, K.A.Shick, K.A.Xavier, R.C.Willson, P.D.Jeffrey, C.Y.Chang, L.C.Sieker, S.Sheriff.
 
  ABSTRACT  
 
The HyHEL-5 antibody has more than a thousandfold lower affinity for bobwhite quail lysozyme (BWQL) than for hen egg-white lysozyme (HEL). Four sequence differences exist between BWQL and HEL, of which only one is involved in the interface with the Fab. The structure of bobwhite quail lysozyme has been determined in the uncomplexed state in two different crystal forms and in the complexed state with HyHEL-5, an antihen egg-white lysozyme Fab. Similar backbone conformations are observed in the three molecules of the two crystal forms of uncomplexed BWQL, although they show considerable variability in side-chain conformation. A relatively mobile segment in uncomplexed BWQL is observed to be part of the HyHEL-5 epitope. No major backbone conformational differences are observed in the lysozyme upon complex formation, but side-chain conformational differences are seen in surface residues that are involved in the interface with the antibody. The hydrogen bonding in the interface between BWQL and HyHEL-5 is similar to that in previously determined lysozyme-HyHEL-5 complexes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17712773 P.Scheerer, A.Kramer, L.Otte, M.Seifert, H.Wessner, C.Scholz, N.Krauss, J.Schneider-Mergener, and W.Höhne (2007).
Structure of an anti-cholera toxin antibody Fab in complex with an epitope-derived D-peptide: a case of polyspecific recognition.
  J Mol Recognit, 20, 263-274.
PDB code: 1zea
16381978 A.Schlessinger, Y.Ofran, G.Yachdav, and B.Rost (2006).
Epitome: database of structure-inferred antigenic epitopes.
  Nucleic Acids Res, 34, D777-D780.  
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
11967357 C.N.Patel, S.M.Noble, G.T.Weatherly, A.Tripathy, D.J.Winzor, and G.J.Pielak (2002).
Effects of molecular crowding by saccharides on alpha-chymotrypsin dimerization.
  Protein Sci, 11, 997.  
11418760 M.C.Vaney, I.Broutin, P.Retailleau, A.Douangamath, S.Lafont, C.Hamiaux, T.Prangé, A.Ducruix, and M.Riès-Kautt (2001).
Structural effects of monovalent anions on polymorphic lysozyme crystals.
  Acta Crystallogr D Biol Crystallogr, 57, 929-940.
PDB codes: 1b0d 1b2k 1hf4 1lcn
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
10737939 D.W.Ritchie, and G.J.Kemp (2000).
Protein docking using spherical polar Fourier correlations.
  Proteins, 39, 178-194.  
9753694 Y.A.Muller, Y.Chen, H.W.Christinger, B.Li, B.C.Cunningham, H.B.Lowman, and A.M.de Vos (1998).
VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface.
  Structure, 6, 1153-1167.
PDB code: 1bj1
9336207 K.A.Xavier, K.A.Shick, S.J.Smith-Gil, and R.C.Willson (1997).
Involvement of water molecules in the association of monoclonal antibody HyHEL-5 with bobwhite quail lysozyme.
  Biophys J, 73, 2116-2125.  
9413990 T.Keitel, A.Kramer, H.Wessner, C.Scholz, J.Schneider-Mergener, and W.Höhne (1997).
Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity.
  Cell, 91, 811-820.
PDB codes: 1bog 1cfn 1cfq 1cfs 1cft 1hi6
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