PDBsum entry 2hkf

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Immune system PDB id
Protein chains
219 a.a. *
210 a.a. *
Waters ×303
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of the complex fab m75- peptide
Structure: Immunoglobulin light chain fab fragment. Chain: l. Immunoglobulin heavy chain fab fragment. Chain: h. Carbonic anhydrase 9. Chain: p. Synonym: carbonic anhydrase ix, carbonate dehydratase ix, c caix, membrane antigen mn, p54/58n, renal cell carcinoma-as antigen g250, rcc-associated antigen g250, pmw1.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Cell: hybridoma cells. Synthetic: yes. Other_details: the peptide was chemically synthesized. The of the peptide is naturally found in homo sapiens (human).
2.01Å     R-factor:   0.179     R-free:   0.242
Authors: V.Kral,P.Mader,R.Stouracova,M.Fabry,M.Horejsi,J.Brynda
Key ref:
V.Král et al. (2008). Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations. Proteins, 71, 1275-1287. PubMed id: 18041760 DOI: 10.1002/prot.21821
04-Jul-06     Release date:   13-Nov-07    
Go to PROCHECK summary

Protein chain
No UniProt id for this chain
Struc: 219 a.a.
Protein chain
No UniProt id for this chain
Struc: 210 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains : E.C.  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
Bound ligand (Het Group name = GLY)
matches with 60.00% similarity
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site


    Added reference    
DOI no: 10.1002/prot.21821 Proteins 71:1275-1287 (2008)
PubMed id: 18041760  
Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations.
V.Král, P.Mader, R.Collard, M.Fábry, M.Horejsí, P.Rezácová, M.Kozísek, J.Závada, J.Sedlácek, L.Rulísek, J.Brynda.
Specific antibodies interfere with the function of human tumor-associated carbonic anhydrase IX (CA IX), and show potential as tools for anticancer interventions. In this work, a correlation between structural elements and thermodynamic parameters of the association of antibody fragment Fab M75 to a peptide corresponding to its epitope in the proteoglycan-like domain of CA IX, is presented. Comparisons of the crystal structures of free Fab M75 and its complex with the epitope peptide reveal major readjustments of CDR-H1 and CDR-H3. In contrast, the overall conformations and positions of CDR-H2 and CDR-L2 remain unaltered, and their positively charged residues may thus present a fixed frame for epitope recognition. Adoption of the altered CDR-H3 conformation in the structure of the complex is accompanied by an apparent local stabilization. Analysis of domain mobility with translation-libration-screw (TLS) method shows that librations of the entire heavy chain variable domain (V(H)) decrease and reorient in the complex, which correlates well with participation of the heavy chain in ligand binding. Isothermal titration microcalorimetry (ITC) experiments revealed a highly unfavorable entropy term, which can be attributed mainly to the decrease in the degrees of freedom of the system, the loss of conformational freedom of peptide and partially to a local stabilization of CDR-H3. Moreover, it was observed that one proton is transferred from the environment to the protein-ligand complex upon binding. Molecular dynamics simulations followed by molecular mechanics/generalized Born surface area (MM-GBSA) calculations of the ligand (epitope peptide) binding energy yielded energy values that were in agreement with the ITC measurements and indicated that the charged residues play crucial role in the epitope binding. Theoretical arguments presented in this work indicate that two adjacent arginine residues (ArgH50 and ArgH52) are responsible for the observed proton transfer.
  Selected figure(s)  
Figure 2.
Figure 2. Average values of residual atomic displacement parameters of the peptide residues in complex.
Figure 5.
Figure 5. Residual atomic displacement parameters of C atoms of the heavy chain residues. Free Fab, full squares; complex, open circles. Horizontal bars indicate CDRs H1, H2, and H3. Two dashed lines show the average of atomic displacement parameters for the heavy chain of free and complexed Fab.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 1275-1287) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21280707 T.Miyata, Y.Ikuta, and F.Hirata (2011).
Free energy calculation using molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate.
  J Chem Phys, 134, 044127.  
20213668 R.J.Falconer, A.Penkova, I.Jelesarov, and B.M.Collins (2010).
Survey of the year 2008: applications of isothermal titration calorimetry.
  J Mol Recognit, 23, 395-413.  
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