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Contents |
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214 a.a.
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215 a.a.
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129 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Complex(antibody-antigen)
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Title:
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Structure of an antibody-antigen complex. Crystal structure of the hy/hel-10 fab-lysozyme complex
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Structure:
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Hyhel-10 igg1 fab (light chain). Chain: l. Engineered: yes. Hyhel-10 igg1 fab (heavy chain). Chain: h. Engineered: yes. Hen egg white lysozyme. Chain: y. Engineered: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Gallus gallus. Chicken. Organism_taxid: 9031
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Biol. unit:
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Trimer (from
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Resolution:
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Authors:
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E.A.Padlan,D.R.Davies
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Key ref:
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E.A.Padlan
et al.
(1989).
Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.
Proc Natl Acad Sci U S A,
86,
5938-5942.
PubMed id:
DOI:
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Date:
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11-Aug-88
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Release date:
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12-Jul-89
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PROCHECK
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Headers
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References
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No UniProt id for this chain
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Enzyme class:
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Chain Y:
E.C.3.2.1.17
- lysozyme.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
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DOI no:
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Proc Natl Acad Sci U S A
86:5938-5942
(1989)
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PubMed id:
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| |
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Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.
|
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E.A.Padlan,
E.W.Silverton,
S.Sheriff,
G.H.Cohen,
S.J.Smith-Gill,
D.R.Davies.
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ABSTRACT
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The crystal structure of the complex of the anti-lysozyme HyHEL-10 Fab and hen
egg white lysozyme has been determined to a nominal resolution of 3.0 A. The
antigenic determinant (epitope) on the lysozyme is discontinuous, consisting of
residues from four different regions of the linear sequence. It consists of the
exposed residues of an alpha-helix together with surrounding amino acids. The
epitope crosses the active-site cleft and includes a tryptophan located within
this cleft. The combining site of the antibody is mostly flat with a
protuberance made up of two tyrosines that penetrate the cleft. All six
complementarity-determining regions of the Fab contribute at least one residue
to the binding; one residue from the framework is also in contact with the
lysozyme. The contacting residues on the antibody contain a disproportionate
number of aromatic side chains. The antibody-antigen contact mainly involves
hydrogen bonds and van der Waals interactions; there is one ion-pair interaction
but it is weak.
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Literature references that cite this PDB file's key reference
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| |
PubMed id
|
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Reference
|
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|
|
|
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A.Pomés
(2010).
Relevant B cell epitopes in allergic disease.
|
| |
Int Arch Allergy Immunol,
152,
1.
|
|
|
|
|
|
|
A.Yokota,
K.Tsumoto,
M.Shiroishi,
T.Nakanishi,
H.Kondo,
and
I.Kumagai
(2010).
Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme.
|
| |
J Biol Chem,
285,
7686-7696.
|
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|
PDB codes:
|
|
|
|
|
|
|
|
S.L.Cox,
J.Stolp,
N.L.Hallahan,
J.Counotte,
W.Zhang,
D.V.Serreze,
A.Basten,
and
P.A.Silveira
(2010).
Enhanced responsiveness to T-cell help causes loss of B-lymphocyte tolerance to a β-cell neo-self-antigen in type 1 diabetes prone NOD mice.
|
| |
Eur J Immunol,
40,
3413-3425.
|
|
|
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|
|
T.D.Chan,
S.Gardam,
D.Gatto,
V.M.Turner,
J.Silke,
and
R.Brink
(2010).
In vivo control of B-cell survival and antigen-specific B-cell responses.
|
| |
Immunol Rev,
237,
90.
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C.E.Leysath,
A.F.Monzingo,
J.A.Maynard,
J.Barnett,
G.Georgiou,
B.L.Iverson,
and
J.D.Robertus
(2009).
Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen.
|
| |
J Mol Biol,
387,
680-693.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
K.L.Randall,
T.Lambe,
A.Johnson,
B.Treanor,
E.Kucharska,
H.Domaschenz,
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L.E.Tze,
A.Enders,
T.L.Crockford,
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D.Alston,
J.G.Cyster,
M.J.Lenardo,
F.Mackay,
E.K.Deenick,
S.G.Tangye,
T.D.Chan,
T.Camidge,
R.Brink,
C.G.Vinuesa,
F.D.Batista,
R.J.Cornall,
and
C.C.Goodnow
(2009).
Dock8 mutations cripple B cell immunological synapses, germinal centers and long-lived antibody production.
|
| |
Nat Immunol,
10,
1283-1291.
|
|
|
|
|
|
|
S.Mohan,
K.Kourentzi,
K.A.Schick,
C.Uehara,
C.A.Lipschultz,
M.Acchione,
M.E.Desantis,
S.J.Smith-Gill,
and
R.C.Willson
(2009).
Association energetics of cross-reactive and specific antibodies.
|
| |
Biochemistry,
48,
1390-1398.
|
|
|
|
|
|
|
K.Kourentzi,
M.Srinivasan,
S.J.Smith-Gill,
and
R.C.Willson
(2008).
Conformational flexibility and kinetic complexity in antibody-antigen interactions.
|
| |
J Mol Recognit,
21,
114-121.
|
|
|
|
|
|
|
M.Garcia-Boronat,
C.M.Diez-Rivero,
E.L.Reinherz,
and
P.A.Reche
(2008).
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
|
| |
Nucleic Acids Res,
36,
W35-W41.
|
|
|
|
|
|
|
R.Brink,
T.G.Phan,
D.Paus,
and
T.D.Chan
(2008).
Visualizing the effects of antigen affinity on T-dependent B-cell differentiation.
|
| |
Immunol Cell Biol,
86,
31-39.
|
|
|
|
|
|
|
T.Nakanishi,
K.Tsumoto,
A.Yokota,
H.Kondo,
and
I.Kumagai
(2008).
Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10.
|
| |
Protein Sci,
17,
261-270.
|
|
|
PDB codes:
|
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|
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|
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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.
|
|
|
|
|
|
|
D.Paus,
T.G.Phan,
T.D.Chan,
S.Gardam,
A.Basten,
and
R.Brink
(2006).
Antigen recognition strength regulates the choice between extrafollicular plasma cell and germinal center B cell differentiation.
|
| |
J Exp Med,
203,
1081-1091.
|
|
|
|
|
|
|
H.Younus,
S.Jamal,
B.Ahmad,
and
M.Saleemuddin
(2006).
Investigation of conformational changes induced by binding of pancreatic RNase to anti-RNase IgG derived Fab monomer using optical procedures.
|
| |
Biochemistry (Mosc),
71,
218-221.
|
|
|
|
|
|
|
P.Haste Andersen,
M.Nielsen,
and
O.Lund
(2006).
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.
|
| |
Protein Sci,
15,
2558-2567.
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|
|
P.M.Oliver,
T.Vass,
J.Kappler,
and
P.Marrack
(2006).
Loss of the proapoptotic protein, Bim, breaks B cell anergy.
|
| |
J Exp Med,
203,
731-741.
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|
|
|
|
|
R.J.Duquesnoy
(2006).
A structurally based approach to determine HLA compatibility at the humoral immune level.
|
| |
Hum Immunol,
67,
847-862.
|
|
|
|
|
|
|
D.Davies,
and
D.Davies
(2005).
A quiet life with proteins.
|
| |
Annu Rev Biophys Biomol Struct,
34,
1.
|
|
|
|
|
|
|
D.Segal,
and
M.Eisenstein
(2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
|
| |
Proteins,
59,
580-591.
|
|
|
|
|
|
|
A.Berchanski,
B.Shapira,
and
M.Eisenstein
(2004).
Hydrophobic complementarity in protein-protein docking.
|
| |
Proteins,
56,
130-142.
|
|
|
|
|
|
|
A.Cauerhff,
F.A.Goldbaum,
and
B.C.Braden
(2004).
Structural mechanism for affinity maturation of an anti-lysozyme antibody.
|
| |
Proc Natl Acad Sci U S A,
101,
3539-3544.
|
|
|
PDB code:
|
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|
|
|
|
|
|
S.Liu,
C.Zhang,
H.Zhou,
and
Y.Zhou
(2004).
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.
|
| |
Proteins,
56,
93.
|
|
|
|
|
|
|
C.L.Adams,
M.K.Macleod,
E.James Milner-White,
R.Aitken,
P.Garside,
and
D.I.Stott
(2003).
Complete analysis of the B-cell response to a protein antigen, from in vivo germinal centre formation to 3-D modelling of affinity maturation.
|
| |
Immunology,
108,
274-287.
|
|
|
|
|
|
|
M.Adachi,
Y.Kurihara,
H.Nojima,
M.Takeda-Shitaka,
K.Kamiya,
and
H.Umeyama
(2003).
Interaction between the antigen and antibody is controlled by the constant domains: normal mode dynamics of the HEL-HyHEL-10 complex.
|
| |
Protein Sci,
12,
2125-2131.
|
|
|
|
|
|
|
S.Mohan,
N.Sinha,
and
S.J.Smith-Gill
(2003).
Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity.
|
| |
Biophys J,
85,
3221-3236.
|
|
|
|
|
|
|
A.Heifetz,
E.Katchalski-Katzir,
and
M.Eisenstein
(2002).
Electrostatics in protein-protein docking.
|
| |
Protein Sci,
11,
571-587.
|
|
|
|
|
|
|
B.O'Nuallain,
and
R.Wetzel
(2002).
Conformational Abs recognizing a generic amyloid fibril epitope.
|
| |
Proc Natl Acad Sci U S A,
99,
1485-1490.
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|
E.B.Plüger,
M.Boes,
C.Alfonso,
C.J.Schröter,
H.Kalbacher,
H.L.Ploegh,
and
C.Driessen
(2002).
Specific role for cathepsin S in the generation of antigenic peptides in vivo.
|
| |
Eur J Immunol,
32,
467-476.
|
|
|
|
|
|
|
J.Pons,
J.R.Stratton,
and
J.F.Kirsch
(2002).
How do two unrelated antibodies, HyHEL-10 and F9.13.7, recognize the same epitope of hen egg-white lysozyme?
|
| |
Protein Sci,
11,
2308-2315.
|
|
|
|
|
|
|
L.Jiang,
Y.Gao,
F.Mao,
Z.Liu,
and
L.Lai
(2002).
Potential of mean force for protein-protein interaction studies.
|
| |
Proteins,
46,
190-196.
|
|
|
|
|
|
|
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.
|
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|
|
V.D.Bowman,
E.S.Chase,
A.W.Franz,
P.R.Chipman,
X.Zhang,
K.L.Perry,
T.S.Baker,
and
T.J.Smith
(2002).
An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons.
|
| |
J Virol,
76,
12250-12258.
|
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|
|
K.Rosner,
D.B.Winter,
R.E.Tarone,
G.L.Skovgaard,
V.A.Bohr,
and
P.J.Gearhart
(2001).
Third complementarity-determining region of mutated VH immunoglobulin genes contains shorter V, D, J, P, and N components than non-mutated genes.
|
| |
Immunology,
103,
179-187.
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|
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M.E.Bloom,
S.M.Best,
S.F.Hayes,
R.D.Wells,
J.B.Wolfinbarger,
R.McKenna,
and
M.Agbandje-McKenna
(2001).
Identification of aleutian mink disease parvovirus capsid sequences mediating antibody-dependent enhancement of infection, virus neutralization, and immune complex formation.
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| |
J Virol,
75,
11116-11127.
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|
|
|
M.Kawahara,
A.Natsume,
S.Terada,
K.Kato,
K.Tsumoto,
I.Kumagai,
M.Miki,
W.Mahoney,
H.Ueda,
and
T.Nagamune
(2001).
Replacing factor-dependency with that for lysozyme: affordable culture of IL-6-dependent hybridoma by transfecting artificial cell surface receptor.
|
| |
Biotechnol Bioeng,
74,
416-423.
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|
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|
|
|
Y.Li,
C.A.Lipschultz,
S.Mohan,
and
S.J.Smith-Gill
(2001).
Mutations of an epitope hot-spot residue alter rate limiting steps of antigen-antibody protein-protein associations.
|
| |
Biochemistry,
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|
|
|
A.Rajpal,
and
J.F.Kirsch
(2000).
Role of the minor energetic determinants of chicken egg white lysozyme (HEWL) to the stability of the HEWL.antibody scFv-10 complex.
|
| |
Proteins,
40,
49-57.
|
|
|
|
|
|
|
D.W.Ritchie,
and
G.J.Kemp
(2000).
Protein docking using spherical polar Fourier correlations.
|
| |
Proteins,
39,
178-194.
|
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|
|
L.M.Wright,
A.M.Brzozowski,
R.E.Hubbard,
A.C.Pike,
S.M.Roberts,
R.N.Skovgaard,
I.Svendsen,
H.Vissing,
and
R.P.Bywater
(2000).
Structure of Fab hGR-2 F6, a competitive antagonist of the glucagon receptor.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
573-580.
|
|
|
PDB code:
|
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|
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|
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|
|
S.L.Pogue,
and
C.C.Goodnow
(2000).
Gene dose-dependent maturation and receptor editing of B cells expressing immunoglobulin (Ig)G1 or IgM/IgG1 tail antigen receptors.
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(2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
|
| |
Biochemistry,
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6296-6309.
|
|
|
PDB codes:
|
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|
|
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|
|
G.Moont,
H.A.Gabb,
and
M.J.Sternberg
(1999).
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| |
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J.M.van Den Elsen,
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D.R.Rose
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Antibody C219 recognizes an alpha-helical epitope on P-glycoprotein.
|
| |
Proc Natl Acad Sci U S A,
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|
PDB code:
|
|
|
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|
|
|
J.Pons,
A.Rajpal,
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| |
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| |
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L.W.Guddat,
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|
| |
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|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Rajpal,
M.G.Taylor,
and
J.F.Kirsch
(1998).
Quantitative evaluation of the chicken lysozyme epitope in the HyHEL-10 Fab complex: free energies and kinetics.
|
| |
Protein Sci,
7,
1868-1874.
|
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|
|
F.D.Batista,
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(1998).
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| |
Immunity,
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K.A.Xavier,
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(1998).
Association and dissociation kinetics of anti-hen egg lysozyme monoclonal antibodies HyHEL-5 and HyHEL-10.
|
| |
Biophys J,
74,
2036-2045.
|
|
|
|
|
|
|
M.G.Taylor,
A.Rajpal,
and
J.F.Kirsch
(1998).
Kinetic epitope mapping of the chicken lysozyme.HyHEL-10 Fab complex: delineation of docking trajectories.
|
| |
Protein Sci,
7,
1857-1867.
|
|
|
|
|
|
|
P.S.Pruett,
and
G.M.Air
(1998).
Critical interactions in binding antibody NC41 to influenza N9 neuraminidase: amino acid contacts on the antibody heavy chain.
|
| |
Biochemistry,
37,
10660-10670.
|
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|
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|
|
T.Keiber-Emmons,
Q.Fang,
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M.K.Crow,
P.Lotke,
and
W.V.Williams
(1998).
Structural motifs in rheumatoid T-cell receptors.
|
| |
DNA Cell Biol,
17,
133-149.
|
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|
T.R.Transue,
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M.A.Ghahroudi,
L.Wyns,
and
S.Muyldermans
(1998).
Camel single-domain antibody inhibits enzyme by mimicking carbohydrate substrate.
|
| |
Proteins,
32,
515-522.
|
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|
X.Ysern,
H.Li,
and
R.A.Mariuzza
(1998).
Imperfect interfaces.
|
| |
Nat Struct Biol,
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|
I.A.Wilson,
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(1997).
T-cell receptor structure and TCR complexes.
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| |
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J.L.Pellequer,
and
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(1997).
Does conformational free energy distinguish loop conformations in proteins?
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| |
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J.S.Harrison,
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M.J.Berry,
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Int Rev Immunol,
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Preparation and crystallization of a human immunodeficiency virus p24-Fab complex.
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E.A.Padlan
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On the nature of antibody combining sites: unusual structural features that may confer on these sites an enhanced capacity for binding ligands.
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Proteins,
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G.M.Air,
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and
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J Virol,
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P.M.Alzari,
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Three-dimensional structure determination of an anti-2-phenyloxazolone antibody: the role of somatic mutation and heavy/light chain pairing in the maturation of an immune response.
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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.
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Links
