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Immunoglobulin PDB id
1ad0
Jmol
Contents
Protein chains
213 a.a. *
220 a.a. *
Waters ×130
* Residue conservation analysis
PDB id:
1ad0
Name: Immunoglobulin
Title: Fab fragment of engineered human monoclonal antibody a5b7
Structure: Antibody a5b7 (light chain). Chain: a, c. Fragment: fab fragment. Engineered: yes. Antibody a5b7 (heavy chain). Chain: b, d. Fragment: fab fragment. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: mus musculus. Expression_system_taxid: 10090. Expression_system_cell: nso cells. Expression_system_cell: nso cells
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.209     R-free:   0.262
Authors: M.J.Banfield,R.L.Brady
Key ref: M.J.Banfield et al. (1997). VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs. Proteins, 29, 161-171. PubMed id: 9329081 DOI: 10.1002/(SICI)1097-0134(199710)29:2<161::AID-PROT4>3.0.CO;2-G
Date:
19-Feb-97     Release date:   25-Feb-98    
PROCHECK
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 Headers
 References

 

 
DOI no: 10.1002/(SICI)1097-0134(199710)29:2<161::AID-PROT4>3.0.CO;2-G Proteins 29:161-171 (1997)
PubMed id: 9329081  
 
 
VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs.
M.J.Banfield, D.J.King, A.Mountain, R.L.Brady.
 
  ABSTRACT  
 
The crystal structures of two pairs of Fab fragments have been determined. The pairs comprise both a murine and an engineered human form, each derived from the antitumor antibodies A5B7 and CTM01. Although antigen specificity is maintained within the pairs, antigen affinity varies. A comparison of the hypervariable loops for each pair of antibodies shows their structure has been well maintained in grafting, supporting the canonical loop model. Detailed structural analysis of the binding sites and domain arrangements for these antibodies suggests the differences in antigen affinity observed are likely to be due to inherent flexibility of the hypervariable loops and movements at the VL:VH domain interface. The four structures provide the first opportunity to study in detail the effects of protein engineering on specific antibodies.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19062174 A.Sivasubramanian, A.Sircar, S.Chaudhury, and J.J.Gray (2009).
Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking.
  Proteins, 74, 497-514.  
17395584 J.Du, H.Wang, C.Zhong, B.Peng, M.Zhang, B.Li, S.Huo, Y.Guo, and J.Ding (2007).
Structural basis for recognition of CD20 by therapeutic antibody Rituximab.
  J Biol Chem, 282, 15073-15080.
PDB code: 2osl
15837620 S.Li, K.R.Schmitz, P.D.Jeffrey, J.J.Wiltzius, P.Kussie, and K.M.Ferguson (2005).
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab.
  Cancer Cell, 7, 301-311.
PDB codes: 1yy8 1yy9
15152083 E.Carredano, H.Baumann, A.Grönberg, N.Norrman, G.Glad, J.Zou, O.Ersoy, E.Steensma, and A.Axén (2004).
A novel and conserved pocket of human kappa-Fab fragments: design, synthesis, and verification of directed affinity ligands.
  Protein Sci, 13, 1476-1488.  
15507619 R.Varghese, Y.Mikyas, P.L.Stewart, and R.Ralston (2004).
Postentry neutralization of adenovirus type 5 by an antihexon antibody.
  J Virol, 78, 12320-12332.  
12833565 E.Vargas-Madrazo, and E.Paz-García (2003).
An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues.
  J Mol Recognit, 16, 113-120.  
12610629 H.S.Cho, K.Mason, K.X.Ramyar, A.M.Stanley, S.B.Gabelli, D.W.Denney, and D.J.Leahy (2003).
Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab.
  Nature, 421, 756-760.
PDB codes: 1n8y 1n8z
12499636 H.Haruyama, S.Ito, K.Miyadai, T.Takahashi, R.Kawaida, T.Takayama, H.Hanzawa, T.Hata, J.Yamaguchi, H.Yoshida-Kato, K.Ichikawa, J.Ohsumi, S.Yonehara, and N.Serizawa (2002).
Humanization of the mouse anti-Fas antibody HFE7A and crystal structure of the humanized HFE7A Fab fragment.
  Biol Pharm Bull, 25, 1537-1545.
PDB code: 1it9
11599031 M.B.Berry, K.A.Johnson, W.Radding, M.Fung, R.Liou, and G.N.Phillips (2001).
Structure of an anti-HIV monoclonal Fab antibody fragment specific to a gp120 C-4 region peptide.
  Proteins, 45, 281-282.
PDB code: 1il1
11701516 J.Maynard, and G.Georgiou (2000).
Antibody engineering.
  Annu Rev Biomed Eng, 2, 339-376.  
10585914 B.Carrasco, J.G.de la Torre, O.Byron, D.King, C.Walters, S.Jones, and S.E.Harding (1999).
Novel size-independent modeling of the dilute solution conformation of the immunoglobulin IgG Fab' domain using SOLPRO and ELLIPS.
  Biophys J, 77, 2902-2910.  
10354514 J.Wally, G.Kica, Y.Zhang, T.Ericsson, L.H.Connors, M.D.Benson, J.J.Liepnieks, J.Murray, M.Skinner, and R.L.Comenzo (1999).
Identification of a novel substitution in the constant region of a gene coding for an amyloidogenic kappa1 light chain.
  Biochim Biophys Acta, 1454, 49-56.  
  10439113 S.Odani, Y.Komori, and F.Gejyo (1999).
Structural analysis of the amyloidogenic kappa Bence Jones protein (FUR).
  Amyloid, 6, 77-88.  
  9696818 B.D.Zelus, D.R.Wessner, R.K.Williams, M.N.Pensiero, F.T.Phibbs, M.deSouza, G.S.Dveksler, and K.V.Holmes (1998).
Purified, soluble recombinant mouse hepatitis virus receptor, Bgp1(b), and Bgp2 murine coronavirus receptors differ in mouse hepatitis virus binding and neutralizing activities.
  J Virol, 72, 7237-7244.  
  9720265 P.J.Hudson (1998).
Recombinant antibody fragments.
  Curr Opin Biotechnol, 9, 395-402.  
9729735 W.Dall'Acqua, and P.Carter (1998).
Antibody engineering.
  Curr Opin Struct Biol, 8, 443-450.  
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 code is shown on the right.