|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
214 a.a.
|
|
|
|
|
|
|
|
|
|
|
218 a.a.
|
|
|
|
|
|
|
|
|
|
|
129 a.a.
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Complex (antibody-antigen)
|
|
|
Title:
|
|
Crystallographic refinement of the three-dimensional structure of the fab d1.3-lysozyme complex at 2.5-angstroms resolution
|
|
Structure:
|
|
Igg1-kappa d1.3 fab (light chain). Chain: l. Engineered: yes. Igg1-kappa d1.3 fab (heavy chain). Chain: h. Engineered: yes. Hen egg white lysozyme. Chain: y. 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
)
|
|
Resolution:
|
|
|
|
Authors:
|
|
T.O.Fischmann,R.J.Poljak
|
|
Key ref:
|
|
T.O.Fischmann
et al.
(1991).
Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution.
J Biol Chem,
266,
12915-12920.
PubMed id:
|
|
|
Date:
|
|
|
27-Aug-90
|
Release date:
|
15-Oct-91
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P01837
(IGKC_MOUSE) -
Immunoglobulin kappa constant from Mus musculus
|
|
|
|
Seq:
Struc:
|
|
|
|
107 a.a.
214 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chain Y:
E.C.3.2.1.17
- lysozyme.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
J Biol Chem
266:12915-12920
(1991)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution.
|
|
T.O.Fischmann,
G.A.Bentley,
T.N.Bhat,
G.Boulot,
R.A.Mariuzza,
S.E.Phillips,
D.Tello,
R.J.Poljak.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The three-dimensional crystal structure of the complex between the Fab from the
monoclonal anti-lysozyme antibody D1.3 and the antigen, hen egg white lysozyme,
has been refined by crystallographic techniques using x-ray intensity data to
2.5-A resolution. The antibody contacts the antigen with residues from all its
complementarity determining regions. Antigen residues 18-27 and 117-125 form a
discontinuous antigenic determinant making hydrogen bonds and van der Waals
interactions with the antibody. Water molecules at or near the antigen-antibody
interface mediate some contacts between antigen and antibody. The fine
specificity of antibody D1.3, which does not bind (K alpha less than 10(5) M-1)
avian lysozymes where Gln121 in the amino acid sequence is occupied by His, can
be explained on the basis of the refined model.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
M.B.Irving,
L.Craig,
A.Menendez,
B.P.Gangadhar,
M.Montero,
N.E.van Houten,
and
J.K.Scott
(2010).
Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes.
|
| |
Mol Immunol,
47,
1137-1148.
|
|
|
|
|
|
|
P.Robert,
L.Limozin,
A.Pierres,
and
P.Bongrand
(2009).
Biomolecule association rates do not provide a complete description of bond formation.
|
| |
Biophys J,
96,
4642-4650.
|
|
|
|
|
|
|
S.A.Richman,
D.H.Aggen,
M.L.Dossett,
D.L.Donermeyer,
P.M.Allen,
P.D.Greenberg,
and
D.M.Kranz
(2009).
Structural features of T cell receptor variable regions that enhance domain stability and enable expression as single-chain ValphaVbeta fragments.
|
| |
Mol Immunol,
46,
902-916.
|
|
|
|
|
|
|
E.O.Saphire,
M.Montero,
A.Menendez,
N.E.van Houten,
M.B.Irving,
R.Pantophlet,
M.B.Zwick,
P.W.Parren,
D.R.Burton,
J.K.Scott,
and
I.A.Wilson
(2007).
Structure of a high-affinity "mimotope" peptide bound to HIV-1-neutralizing antibody b12 explains its inability to elicit gp120 cross-reactive antibodies.
|
| |
J Mol Biol,
369,
696-709.
|
|
|
|
|
|
|
G.E.Gómez,
A.Cauerhff,
P.O.Craig,
F.A.Goldbaum,
and
J.M.Delfino
(2006).
Exploring protein interfaces with a general photochemical reagent.
|
| |
Protein Sci,
15,
744-752.
|
|
|
|
|
|
|
R.J.Duquesnoy
(2006).
A structurally based approach to determine HLA compatibility at the humoral immune level.
|
| |
Hum Immunol,
67,
847-862.
|
|
|
|
|
|
|
S.S.Mohapatra,
R.F.Lockey,
and
S.Shirley
(2005).
Immunobiology of grass pollen allergens.
|
| |
Curr Allergy Asthma Rep,
5,
381-387.
|
|
|
|
|
|
|
U.Kulkarni-Kale,
S.Bhosle,
and
A.S.Kolaskar
(2005).
CEP: a conformational epitope prediction server.
|
| |
Nucleic Acids Res,
33,
W168-W171.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
R.Kuroki,
M.Hirose,
Y.Kato,
M.D.Feese,
T.Tamada,
H.Shigematsu,
H.Watarai,
Y.Maeda,
T.Tahara,
T.Kato,
and
H.Miyazaki
(2002).
Crystallization of the functional domain of human thrombopoietin using an antigen-binding fragment derived from neutralizing monoclonal antibody.
|
| |
Acta Crystallogr D Biol Crystallogr,
58,
856-858.
|
|
|
|
|
|
|
F.Bettsworth,
C.Monnet,
B.Watelet,
N.Battail-Poirot,
B.Gilquin,
M.Jolivet,
A.Menez,
M.Arnaud,
and
F.Ducancel
(2001).
Functional characterization of two anti-estradiol antibodies as deduced from modelling and site-directed mutagenesis experiments.
|
| |
J Mol Recognit,
14,
99.
|
|
|
|
|
|
|
K.Poulas,
E.Eliopoulos,
E.Vatzaki,
J.Navaza,
M.Kontou,
N.Oikonomakos,
K.R.Acharya,
and
S.J.Tzartos
(2001).
Crystal structure of Fab198, an efficient protector of the acetylcholine receptor against myasthenogenic antibodies.
|
| |
Eur J Biochem,
268,
3685-3693.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Norel,
F.Sheinerman,
D.Petrey,
and
B.Honig
(2001).
Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis.
|
| |
Protein Sci,
10,
2147-2161.
|
|
|
|
|
|
|
J.Kleinjung,
M.C.Petit,
P.Orlewski,
A.Mamalaki,
S.J.Tzartos,
V.Tsikaris,
M.Sakarellos-Daitsiotis,
C.Sakarellos,
M.Marraud,
and
M.T.Cung
(2000).
The third-dimensional structure of the complex between an Fv antibody fragment and an analogue of the main immunogenic region of the acetylcholine receptor: a combined two-dimensional NMR, homology, and molecular modeling approach.
|
| |
Biopolymers,
53,
113-128.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
S.P.Prewitt,
A.A.Komissarov,
S.L.Deutscher,
and
J.J.Tanner
(2000).
Crystallization and molecular-replacement studies of a recombinant antigen-binding fragment complexed with single-stranded DNA.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
1007-1011.
|
|
|
|
|
|
|
U.Lamminmäki,
and
J.Kankare
(2000).
Crystallization and preliminary X-ray analysis of a recombinant Fab fragment in complex with 17beta-oestradiol.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
1670-1672.
|
|
|
|
|
|
|
G.Moont,
H.A.Gabb,
and
M.J.Sternberg
(1999).
Use of pair potentials across protein interfaces in screening predicted docked complexes.
|
| |
Proteins,
35,
364-373.
|
|
|
|
|
|
|
J.A.Cuff,
and
G.J.Barton
(1999).
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
|
| |
Proteins,
34,
508-519.
|
|
|
|
|
|
|
J.Thatte,
A.Qadri,
C.Radu,
and
E.S.Ward
(1999).
Molecular requirements for T cell recognition by a major histocompatibility complex class II-restricted T cell receptor: the involvement of the fourth hypervariable loop of the Valpha domain.
|
| |
J Exp Med,
189,
509-520.
|
|
|
|
|
|
|
B.C.Braden,
E.R.Goldman,
R.A.Mariuzza,
and
R.J.Poljak
(1998).
Anatomy of an antibody molecule: structure, kinetics, thermodynamics and mutational studies of the antilysozyme antibody D1.3.
|
| |
Immunol Rev,
163,
45-57.
|
|
|
|
|
|
|
A.C.Wallace,
N.Borkakoti,
and
J.M.Thornton
(1997).
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
|
| |
Protein Sci,
6,
2308-2323.
|
|
|
|
|
|
|
J.L.Pellequer,
and
S.W.Chen
(1997).
Does conformational free energy distinguish loop conformations in proteins?
|
| |
Biophys J,
73,
2359-2375.
|
|
|
|
|
|
|
R.Celikel,
Madhusudan,
K.I.Varughese,
M.Shima,
A.Yoshioka,
J.Ware,
and
Z.M.Ruggeri
(1997).
Crystal structure of NMC-4 fab anti-von Willebrand factor A1 domain.
|
| |
Blood Cells Mol Dis,
23,
123-134.
|
|
|
|
|
|
|
D.R.Davies,
and
G.H.Cohen
(1996).
Interactions of protein antigens with antibodies.
|
| |
Proc Natl Acad Sci U S A,
93,
7.
|
|
|
|
|
|
|
F.A.Goldbaum,
F.P.Schwarz,
E.Eisenstein,
A.Cauerhff,
R.A.Mariuzza,
and
R.J.Poljak
(1996).
The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies D1.3 and D44.1.
|
| |
J Mol Recognit,
9,
6.
|
|
|
|
|
|
|
F.Brard,
F.Jovelin,
S.Petit,
F.Tron,
and
D.Gilbert
(1996).
Structural properties and mutation patterns of anti-nucleosome monoclonal antibodies are similar to those of anti-DNA antibodies.
|
| |
Eur J Immunol,
26,
1587-1594.
|
|
|
|
|
|
|
J.M.Verdier,
K.V.Ewart,
M.Griffith,
and
C.L.Hew
(1996).
An immune response to ice crystals in North Atlantic fishes.
|
| |
Eur J Biochem,
241,
740-743.
|
|
|
|
|
|
|
N.C.Singha,
N.Surolia,
and
A.Surolia
(1996).
On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation.
|
| |
Biosci Rep,
16,
1.
|
|
|
|
|
|
|
P.C.Keck,
and
J.S.Huston
(1996).
Symmetry of Fv architecture is conducive to grafting a second antibody binding site in the Fv region.
|
| |
Biophys J,
71,
2002-2011.
|
|
|
|
|
|
|
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,
and
S.Sheriff
(1996).
Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment.
|
| |
Proteins,
26,
55-65.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Spinelli,
L.Frenken,
D.Bourgeois,
L.de Ron,
W.Bos,
T.Verrips,
C.Anguille,
C.Cambillau,
and
M.Tegoni
(1996).
The crystal structure of a llama heavy chain variable domain.
|
| |
Nat Struct Biol,
3,
752-757.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.D.Katayama,
F.J.Eidelman,
A.Duncan,
F.Hooshmand,
and
S.M.Hedrick
(1995).
Predicted complementarity determining regions of the T cell antigen receptor determine antigen specificity.
|
| |
EMBO J,
14,
927-938.
|
|
|
|
|
|
|
C.W.Murray,
D.E.Clark,
and
D.G.Byrne
(1995).
PRO_LIGAND: an approach to de novo molecular design. 6. Flexible fitting in the design of peptides.
|
| |
J Comput Aided Mol Des,
9,
381-395.
|
|
|
|
|
|
|
D.Frenkel,
D.E.Clark,
J.Li,
C.W.Murray,
B.RObson,
B.Waszkowycz,
and
D.R.Westhead
(1995).
PRO_LIGAND: an approach to de novo molecular design. 4. Application to the design of peptides.
|
| |
J Comput Aided Mol Des,
9,
213-225.
|
|
|
|
|
|
|
K.P.Murphy,
E.Freire,
and
Y.Paterson
(1995).
Configurational effects in antibody-antigen interactions studied by microcalorimetry.
|
| |
Proteins,
21,
83-90.
|
|
|
|
|
|
|
L.C.Kovari,
C.Momany,
and
M.G.Rossmann
(1995).
The use of antibody fragments for crystallization and structure determinations.
|
| |
Structure,
3,
1291-1293.
|
|
|
|
|
|
|
M.Viswanathan,
J.M.Anchin,
P.R.Droupadi,
C.Mandal,
D.S.Linthicum,
and
S.Subramaniam
(1995).
Structural predictions of the binding site architecture for monoclonal antibody NC6.8 using computer-aided molecular modeling, ligand binding, and spectroscopy.
|
| |
Biophys J,
69,
741-753.
|
|
|
|
|
|
|
M.W.Wien,
D.J.Filman,
E.A.Stura,
S.Guillot,
F.Delpeyroux,
R.Crainic,
and
J.M.Hogle
(1995).
Structure of the complex between the Fab fragment of a neutralizing antibody for type 1 poliovirus and its viral epitope.
|
| |
Nat Struct Biol,
2,
232-243.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.V.Kashmiri,
L.Shu,
E.A.Padlan,
D.E.Milenic,
J.Schlom,
and
P.H.Hand
(1995).
Generation, characterization, and in vivo studies of humanized anticarcinoma antibody CC49.
|
| |
Hybridoma,
14,
461-473.
|
|
|
|
|
|
|
J.F.Schildbach,
S.Y.Shaw,
R.E.Bruccoleri,
E.Haber,
L.A.Herzenberg,
G.C.Jager,
P.D.Jeffrey,
D.J.Panka,
D.R.Parks,
and
R.I.Near
(1994).
Contribution of a single heavy chain residue to specificity of an anti-digoxin monoclonal antibody.
|
| |
Protein Sci,
3,
737-749.
|
|
|
|
|
|
|
L.Young,
R.L.Jernigan,
and
D.G.Covell
(1994).
A role for surface hydrophobicity in protein-protein recognition.
|
| |
Protein Sci,
3,
717-729.
|
|
|
|
|
|
|
M.Totrov,
and
R.Abagyan
(1994).
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy.
|
| |
Nat Struct Biol,
1,
259-263.
|
|
|
|
|
|
|
T.N.Bhat,
G.A.Bentley,
G.Boulot,
M.I.Greene,
D.Tello,
W.Dall'Acqua,
H.Souchon,
F.P.Schwarz,
R.A.Mariuzza,
and
R.J.Poljak
(1994).
Bound water molecules and conformational stabilization help mediate an antigen-antibody association.
|
| |
Proc Natl Acad Sci U S A,
91,
1089-1093.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Lescar,
M.M.Riottot,
H.Souchon,
V.Chitarra,
G.A.Bentley,
J.Navaza,
P.M.Alzari,
and
R.J.Poljak
(1993).
Crystallization, preliminary X-ray diffraction study, and crystal packing of a complex between anti-hen lysozyme antibody F9.13.7 and guinea-fowl lysozyme.
|
| |
Proteins,
15,
209-212.
|
|
|
|
|
|
|
J.M.Nuss,
P.B.Whitaker,
and
G.M.Air
(1993).
Identification of critical contact residues in the NC41 epitope of a subtype N9 influenza virus neuraminidase.
|
| |
Proteins,
15,
121-132.
|
|
|
|
|
|
|
J.S.Huston,
J.McCartney,
M.S.Tai,
C.Mottola-Hartshorn,
D.Jin,
F.Warren,
P.Keck,
and
H.Oppermann
(1993).
Medical applications of single-chain antibodies.
|
| |
Int Rev Immunol,
10,
195-217.
|
|
|
|
|
|
|
J.White,
A.Pullen,
K.Choi,
P.Marrack,
and
J.W.Kappler
(1993).
Antigen recognition properties of mutant V beta 3+ T cell receptors are consistent with an immunoglobulin-like structure for the receptor.
|
| |
J Exp Med,
177,
119-125.
|
|
|
|
|
|
|
O.Vix,
B.Rees,
J.C.Thierry,
and
D.Altschuh
(1993).
Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody.
|
| |
Proteins,
15,
339-348.
|
|
|
|
|
|
|
P.Holliger,
T.Prospero,
and
G.Winter
(1993).
"Diabodies": small bivalent and bispecific antibody fragments.
|
| |
Proc Natl Acad Sci U S A,
90,
6444-6448.
|
|
|
|
|
|
|
R.L.Stanfield,
M.Takimoto-Kamimura,
J.M.Rini,
A.T.Profy,
and
I.A.Wilson
(1993).
Major antigen-induced domain rearrangements in an antibody.
|
| |
Structure,
1,
83-93.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
V.Chitarra,
P.M.Alzari,
G.A.Bentley,
T.N.Bhat,
J.L.Eiselé,
A.Houdusse,
J.Lescar,
H.Souchon,
and
R.J.Poljak
(1993).
Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex.
|
| |
Proc Natl Acad Sci U S A,
90,
7711-7715.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.A.Borrebaeck,
A.C.Malmborg,
C.Furebring,
A.Michaelsson,
S.Ward,
L.Danielsson,
and
M.Ohlin
(1992).
Kinetic analysis of recombinant antibody-antigen interactions: relation between structural domains and antigen binding.
|
| |
Biotechnology (N Y),
10,
697-698.
|
|
|
|
|
|
|
D.R.Davies,
and
E.A.Padlan
(1992).
Twisting into shape.
|
| |
Curr Biol,
2,
254-256.
|
|
|
|
|
|
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.
|
 |
|
Links
