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Contents |
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* Residue conservation analysis
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J Mol Biol
190:593-604
(1986)
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PubMed id:
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Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A.
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Y.Satow,
G.H.Cohen,
E.A.Padlan,
D.R.Davies.
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ABSTRACT
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The crystal structure of the Fab of McPC603, a phosphocholine-binding mouse
myeloma protein, has been refined at 2.7 A resolution by a combination of
restrained least-squares refinement and molecular modeling. The overall
structure remains as previously reported, with an elbow bend angle between the
variable and constant modules of 133 degrees. Some adjustments have been made in
the structure of the loops as a result of the refinement. The hypervariable
loops are all visible in the electron density map with the exception of three
residues in the first hypervariable loop of the light chain. A sulfate ion
occupies the site of binding of the phosphate moiety of phosphocholine.
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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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C.J.Riley,
K.P.Engelhardt,
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Design and activity of a murine and humanized anti-CEACAM6 single-chain variable fragment in the treatment of pancreatic cancer.
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X-ray crystal structures of human immunodeficiency virus type 1 protease mutants complexed with atazanavir.
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J Virol,
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PDB codes:
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Y.Yan,
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Structural studies of human alkaline phosphatase in complex with strontium: implication for its secondary effect in bones.
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Protein Sci,
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PDB code:
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Y.Singh,
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J Mol Biol,
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Y.Sakurai,
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High thermal stability imparted by a designed tandem Arg-Trp stretch in an alpha-helical coiled coil.
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Angew Chem Int Ed Engl,
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J.C.Peter,
G.Wallukat,
J.Tugler,
D.Maurice,
J.C.Roegel,
J.P.Briand,
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Modulation of the M2 muscarinic acetylcholine receptor activity with monoclonal anti-M2 receptor antibody fragments.
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J Biol Chem,
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M.Graille,
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N.Leulliot,
C.Z.Zhou,
I.Li de la Sierra Gallay,
L.Jacquamet,
J.L.Ferrer,
D.Liger,
A.Poupon,
J.Janin,
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(2004).
Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family.
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| |
Structure,
12,
839-847.
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PDB codes:
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S.Galdiero,
and
E.Gouaux
(2004).
High resolution crystallographic studies of alpha-hemolysin-phospholipid complexes define heptamer-lipid head group interactions: implication for understanding protein-lipid interactions.
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Protein Sci,
13,
1503-1511.
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I.Kumagai,
Y.Nishimiya,
H.Kondo,
and
K.Tsumoto
(2003).
Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10.
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J Biol Chem,
278,
24929-24936.
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PDB codes:
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H.Li,
T.J.Ryan,
K.J.Chave,
and
P.Van Roey
(2002).
Three-dimensional structure of human gamma -glutamyl hydrolase. A class I glatamine amidotransferase adapted for a complex substate.
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J Biol Chem,
277,
24522-24529.
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PDB code:
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I.Pedroso,
M.P.Irún,
C.Machicado,
and
J.Sancho
(2002).
Four-state equilibrium unfolding of an scFv antibody fragment.
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Biochemistry,
41,
9873-9884.
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M.Graille,
S.Harrison,
M.P.Crump,
S.C.Findlow,
N.G.Housden,
B.H.Muller,
N.Battail-Poirot,
G.Sibaï,
B.J.Sutton,
M.J.Taussig,
C.Jolivet-Reynaud,
M.G.Gore,
and
E.A.Stura
(2002).
Evidence for plasticity and structural mimicry at the immunoglobulin light chain-protein L interface.
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J Biol Chem,
277,
47500-47506.
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PDB code:
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M.H.Le Du,
and
J.L.Millan
(2002).
Structural evidence of functional divergence in human alkaline phosphatases.
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J Biol Chem,
277,
49808-49814.
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O.Almog,
D.T.Gallagher,
J.E.Ladner,
S.Strausberg,
P.Alexander,
P.Bryan,
and
G.L.Gilliland
(2002).
Structural basis of thermostability. Analysis of stabilizing mutations in subtilisin BPN'.
|
| |
J Biol Chem,
277,
27553-27558.
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PDB codes:
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R.Samudrala,
and
M.Levitt
(2002).
A comprehensive analysis of 40 blind protein structure predictions.
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| |
BMC Struct Biol,
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A.Addlagatta,
S.Krzywda,
H.Czapinska,
J.Otlewski,
and
M.Jaskolski
(2001).
Ultrahigh-resolution structure of a BPTI mutant.
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| |
Acta Crystallogr D Biol Crystallogr,
57,
649-663.
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PDB code:
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C.Mura,
D.Cascio,
M.R.Sawaya,
and
D.S.Eisenberg
(2001).
The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core.
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| |
Proc Natl Acad Sci U S A,
98,
5532-5537.
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PDB code:
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R.L.Fahrner,
D.Cascio,
J.A.Lake,
and
A.Slesarev
(2001).
An ancestral nuclear protein assembly: crystal structure of the Methanopyrus kandleri histone.
|
| |
Protein Sci,
10,
2002-2007.
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PDB code:
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A.Ricciardi,
M.H.le Du,
M.Khayati,
F.Dajas,
J.C.Boulain,
A.Menez,
and
F.Ducancel
(2000).
Do structural deviations between toxins adopting the same fold reflect functional differences?
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| |
J Biol Chem,
275,
18302-18310.
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C.A.Sotriffer,
B.M.Rode,
J.M.Varga,
and
K.R.Liedl
(2000).
Elbow flexibility and ligand-induced domain rearrangements in antibody Fab NC6.8: large effects of a small hapten.
|
| |
Biophys J,
79,
614-628.
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D.R.Davies,
I.Y.Goryshin,
W.S.Reznikoff,
and
I.Rayment
(2000).
Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.
|
| |
Science,
289,
77-85.
|
|
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PDB codes:
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E.W.Humke,
S.K.Shriver,
M.A.Starovasnik,
W.J.Fairbrother,
and
V.M.Dixit
(2000).
ICEBERG: a novel inhibitor of interleukin-1beta generation.
|
| |
Cell,
103,
99.
|
|
|
PDB code:
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I.Eidhammer,
I.Jonassen,
and
W.R.Taylor
(2000).
Structure comparison and structure patterns.
|
| |
J Comput Biol,
7,
685-716.
|
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J.A.Hardy,
and
H.C.Nelson
(2000).
Proline in alpha-helical kink is required for folding kinetics but not for kinked structure, function, or stability of heat shock transcription factor.
|
| |
Protein Sci,
9,
2128-2141.
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|
PDB codes:
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J.Bajorath
(2000).
Molecular organization, structural features, and ligand binding characteristics of CD44, a highly variable cell surface glycoprotein with multiple functions.
|
| |
Proteins,
39,
103-111.
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M.Brown,
M.A.Schumacher,
G.D.Wiens,
R.G.Brennan,
and
M.B.Rittenberg
(2000).
The structural basis of repertoire shift in an immune response to phosphocholine.
|
| |
J Exp Med,
191,
2101-2112.
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PDB code:
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M.Jäger,
and
A.Plückthun
(2000).
Direct evidence by H/D exchange and ESI-MS for transient unproductive domain interaction in the refolding of an antibody scFv fragment.
|
| |
Protein Sci,
9,
552-563.
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P.B.Furtado,
R.Furmonaviciene,
J.McElveen,
H.F.Sewell,
and
F.Shakib
(2000).
Prediction of the interacting surfaces in a trimolecular complex formed between the major dust mite allergen Der p 1, a mouse monoclonal anti-Der p 1 antibody, and its anti-idiotype.
|
| |
Mol Pathol,
53,
324-332.
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T.Meguro,
T.Kashiwagi,
and
Y.Satow
(2000).
Crystal structure of the low-humidity form of aspartame sweetener.
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J Pept Res,
56,
97.
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A.Roussel,
S.Spinelli,
S.Déret,
J.Navaza,
P.Aucouturier,
and
C.Cambillau
(1999).
The structure of an entire noncovalent immunoglobulin kappa light-chain dimer (Bence-Jones protein) reveals a weak and unusual constant domains association.
|
| |
Eur J Biochem,
260,
192-199.
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PDB code:
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C.D.Thanos,
S.Faham,
K.E.Goodwill,
D.Cascio,
M.Phillips,
and
J.U.Bowie
(1999).
Monomeric structure of the human EphB2 sterile alpha motif domain.
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| |
J Biol Chem,
274,
37301-37306.
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PDB code:
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J.E.Ladner,
N.G.Abdulaev,
D.L.Kakuev,
M.Tordová,
K.D.Ridge,
and
G.L.Gilliland
(1999).
The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
1127-1135.
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PDB code:
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J.L.Pellequer,
S.Chen,
V.A.Roberts,
J.A.Tainer,
and
E.D.Getzoff
(1999).
Unraveling the effect of changes in conformation and compactness at the antibody V(L)-V(H) interface upon antigen binding.
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| |
J Mol Recognit,
12,
267-275.
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J.Vitali,
D.Carroll,
R.G.Chaudhry,
and
M.L.Hackert
(1999).
Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
1978-1985.
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PDB code:
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M.H.Seto,
H.L.Liu,
D.A.Zajchowski,
and
M.Whitlow
(1999).
Protein fold analysis of the B30.2-like domain.
|
| |
Proteins,
35,
235-249.
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N.Kessler,
D.Perl-Treves,
L.Addadi,
and
M.Eisenstein
(1999).
Structural and chemical complementarity between antibodies and the crystal surfaces they recognize.
|
| |
Proteins,
34,
383-394.
|
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|
A.M.Nersissian,
C.Immoos,
M.G.Hill,
P.J.Hart,
G.Williams,
R.G.Herrmann,
and
J.S.Valentine
(1998).
Uclacyanins, stellacyanins, and plantacyanins are distinct subfamilies of phytocyanins: plant-specific mononuclear blue copper proteins.
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| |
Protein Sci,
7,
1915-1929.
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A.Rodríguez-Romero,
O.Almog,
M.Tordova,
Z.Randhawa,
and
G.L.Gilliland
(1998).
Primary and tertiary structures of the Fab fragment of a monoclonal anti-E-selectin 7A9 antibody that inhibits neutrophil attachment to endothelial cells.
|
| |
J Biol Chem,
273,
11770-11775.
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PDB code:
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C.Mazza,
R.Breton,
D.Housset,
and
J.C.Fontecilla-Camps
(1998).
Unusual charge stabilization of NADP+ in 17beta-hydroxysteroid dehydrogenase.
|
| |
J Biol Chem,
273,
8145-8152.
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PDB codes:
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D.T.Gallagher,
G.L.Gilliland,
G.Xiao,
J.Zondlo,
K.E.Fisher,
D.Chinchilla,
and
E.Eisenstein
(1998).
Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase.
|
| |
Structure,
6,
465-475.
|
|
|
PDB code:
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G.B.Vásquez,
X.Ji,
C.Fronticelli,
and
G.L.Gilliland
(1998).
Human carboxyhemoglobin at 2.2 A resolution: structure and solvent comparisons of R-state, R2-state and T-state hemoglobins.
|
| |
Acta Crystallogr D Biol Crystallogr,
54,
355-366.
|
|
|
PDB code:
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|
G.D.Wiens,
V.A.Roberts,
E.A.Whitcomb,
T.O'Hare,
M.P.Stenzel-Poore,
and
M.B.Rittenberg
(1998).
Harmful somatic mutations: lessons from the dark side.
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| |
Immunol Rev,
162,
197-209.
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J.Bajorath,
B.Greenfield,
S.B.Munro,
A.J.Day,
and
A.Aruffo
(1998).
Identification of CD44 residues important for hyaluronan binding and delineation of the binding site.
|
| |
J Biol Chem,
273,
338-343.
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J.Bajorath
(1998).
Detailed comparison of two molecular models of the human CD40 ligand with an x-ray structure and critical assessment of model-based mutagenesis and residue mapping studies.
|
| |
J Biol Chem,
273,
24603-24609.
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J.Kervinen,
J.Lubkowski,
A.Zdanov,
D.Bhatt,
B.M.Dunn,
K.Y.Hui,
D.J.Powell,
J.Kay,
A.Wlodawer,
and
A.Gustchina
(1998).
Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV.
|
| |
Protein Sci,
7,
2314-2323.
|
|
|
PDB codes:
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|
|
L.J.Harris,
S.B.Larson,
E.Skaletsky,
and
A.McPherson
(1998).
Comparison of the conformations of two intact monoclonal antibodies with hinges.
|
| |
Immunol Rev,
163,
35-43.
|
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M.Karavitis,
C.Fronticelli,
W.S.Brinigar,
G.B.Vasquez,
V.Militello,
M.Leone,
and
A.Cupane
(1998).
Properties of human hemoglobins with increased polarity in the alpha- or beta-heme pocket. Carbonmonoxy derivatives.
|
| |
J Biol Chem,
273,
23740-23749.
|
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|
M.P.Lefranc,
V.Giudicelli,
C.Busin,
J.Bodmer,
W.Müller,
R.Bontrop,
M.Lemaitre,
A.Malik,
and
D.Chaume
(1998).
IMGT, the International ImMunoGeneTics database.
|
| |
Nucleic Acids Res,
26,
297-303.
|
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|
|
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|
|
O.Almog,
T.Gallagher,
M.Tordova,
J.Hoskins,
P.Bryan,
and
G.L.Gilliland
(1998).
Crystal structure of calcium-independent subtilisin BPN' with restored thermal stability folded without the prodomain.
|
| |
Proteins,
31,
21-32.
|
|
|
PDB code:
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|
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|
|
|
P.H.Tan,
B.M.Sandmaier,
and
P.S.Stayton
(1998).
Contributions of a highly conserved VH/VL hydrogen bonding interaction to scFv folding stability and refolding efficiency.
|
| |
Biophys J,
75,
1473-1482.
|
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|
|
P.J.Hart,
H.Liu,
M.Pellegrini,
A.M.Nersissian,
E.B.Gralla,
J.S.Valentine,
and
D.Eisenberg
(1998).
Subunit asymmetry in the three-dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis.
|
| |
Protein Sci,
7,
545-555.
|
|
|
PDB code:
|
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|
|
|
|
|
S.Vasudevan,
T.Tsuruo,
and
D.R.Rose
(1998).
Mode of binding of anti-P-glycoprotein antibody MRK-16 to its antigen. A crystallographic and molecular modeling study.
|
| |
J Biol Chem,
273,
25413-25419.
|
|
|
PDB code:
|
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|
|
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|
|
X.Ji,
M.Braxenthaler,
J.Moult,
C.Fronticelli,
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PDB codes:
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D.Pignol,
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Proc Natl Acad Sci U S A,
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Structure,
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PDB codes:
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Cell,
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PDB code:
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Multiple subunits of a voltage-dependent potassium channel contribute to the binding site for tetraethylammonium.
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Neuron,
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Proteins,
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PDB code:
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P.M.Kirkham,
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Ann N Y Acad Sci,
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Proc Natl Acad Sci U S A,
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Proc Natl Acad Sci U S A,
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PDB code:
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H.J.Kreienkamp,
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Proc Natl Acad Sci U S A,
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An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.
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Proteins,
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PDB codes:
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|
M.Shoham,
P.Proctor,
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Crystal parameters and molecular replacement of an anticholera toxin peptide complex.
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Proteins,
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Identification of the region of T cell receptor beta chain that interacts with the self-superantigen MIs-1a.
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The three-dimensional structure of recombinant bovine chymosin at 2.3 A resolution.
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Proteins,
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PDB code:
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J.L.Dul,
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A single amino acid substitution in the variable region of the light chain specifically blocks immunoglobulin secretion.
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Proc Natl Acad Sci U S A,
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Computer analysis of mutations that affect antibody specificity.
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Proteins,
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Biopolymers,
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Proc Natl Acad Sci U S A,
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PDB code:
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Cloning of the immunological repertoire in Escherichia coli for generation of monoclonal catalytic antibodies: construction of a heavy chain variable region-specific cDNA library.
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Three-dimensional structure of Fab R19.9, a monoclonal murine antibody specific for the p-azobenzenearsonate group.
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Proc Natl Acad Sci U S A,
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PDB codes:
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J.S.Huston,
D.Levinson,
M.Mudgett-Hunter,
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Proc Natl Acad Sci U S A,
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PDB code:
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|
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|
R.M.Fine,
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Proteins,
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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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