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PDBsum entry 1bbp
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Bilin binding
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PDB id
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1bbp
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* Residue conservation analysis
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PDB id:
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Bilin binding
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Title:
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Molecular structure of the bilin binding protein (bbp) from pieris brassicae after refinement at 2.0 angstroms resolution.
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Structure:
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Bilin binding protein. Chain: a, b, c, d. Engineered: yes
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Source:
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Pieris brassicae. Large cabbage white. Organism_taxid: 7116
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Biol. unit:
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Tetramer (from
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Resolution:
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Authors:
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R.Huber,M.Schneider,I.Mayr,R.Mueller,R.Deutzmann,F.Suter,H.Zuber, H.Falk,H.Kayser
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Key ref:
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R.Huber
et al.
(1987).
Molecular structure of the bilin binding protein (BBP) from Pieris brassicae after refinement at 2.0 A resolution.
J Mol Biol,
198,
499-513.
PubMed id:
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Date:
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19-Sep-90
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Release date:
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15-Oct-91
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PROCHECK
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Headers
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References
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P09464
(BBP_PIEBR) -
Bilin-binding protein from Pieris brassicae
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Seq:
Struc:
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189 a.a.
173 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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J Mol Biol
198:499-513
(1987)
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PubMed id:
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Molecular structure of the bilin binding protein (BBP) from Pieris brassicae after refinement at 2.0 A resolution.
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R.Huber,
M.Schneider,
I.Mayr,
R.Müller,
R.Deutzmann,
F.Suter,
H.Zuber,
H.Falk,
H.Kayser.
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ABSTRACT
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The bilin binding protein (BBP) from the insect Pieris brassicae has been
analysed for amino acid sequence, spectral properties and three-dimensional
structure. The crystal structure that had been determined by isomorphous
replacement has been refined at 2.0 A (1 A = 0.1 nm) resolution to an R-value of
0.20. The asymmetric unit contains four independent subunits of BBP. The
co-ordinate differences are 0.25 A, in accord with the estimated error in
co-ordinates. The polypeptide chain fold is characterized by an eight-stranded
barrel. The connecting loops splay out at the upper end of the barrel and open
it, whilst the lower end is closed. The overall shape resembles a calyx. The
biliverdin IX gamma chromophore is located in a central cleft at the upper end
of the barrel. The bilatriene moiety is in cyclic helical geometry with
configuration Z,Z,Z and conformation syn,syn,syn. The geometry is in accord with
the spectral properties and permits a correlation between sign of the circular
dichroism bands and sense of the bilatriene helices. The fold of BBP is related
to retinol binding protein (RBP), as had been recognized in the preliminary
analysis, although the amino acid sequences of RBP and BBP show only 10%
homology. There are large differences in the loops at the upper end of the
barrel, whilst the segments of the centre and the lower end of the barrel
superimpose closely. The ligands of BBP and RBP, biliverdin and retinol,
respectively, are also similarly located.
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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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J.L.Mills,
G.Liu,
A.Skerra,
and
T.Szyperski
(2009).
NMR structure and dynamics of the engineered fluorescein-binding lipocalin FluA reveal rigidification of beta-barrel and variable loops upon enthalpy-driven ligand binding.
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Biochemistry,
48,
7411-7419.
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PDB code:
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M.Kupka,
J.Zhang,
W.L.Fu,
J.M.Tu,
S.Böhm,
P.Su,
Y.Chen,
M.Zhou,
H.Scheer,
and
K.H.Zhao
(2009).
Catalytic mechanism of S-type phycobiliprotein lyase: chaperone-like action and functional amino acid residues.
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J Biol Chem,
284,
36405-36414.
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Y.W.Tan,
S.L.Chan,
T.C.Ong,
l.e. .Y.Yit,
Y.S.Tiong,
F.T.Chew,
J.Sivaraman,
and
Y.K.Mok
(2009).
Structures of Two Major Allergens, Bla g 4 and Per a 4, from Cockroaches and Their IgE Binding Epitopes.
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J Biol Chem,
284,
3148-3157.
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PDB codes:
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A.Skerra
(2008).
Alternative binding proteins: anticalins - harnessing the structural plasticity of the lipocalin ligand pocket to engineer novel binding activities.
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FEBS J,
275,
2677-2683.
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N.C.Rockwell,
S.L.Njuguna,
L.Roberts,
E.Castillo,
V.L.Parson,
S.Dwojak,
J.C.Lagarias,
and
S.C.Spiller
(2008).
A second conserved GAF domain cysteine is required for the blue/green photoreversibility of cyanobacteriochrome Tlr0924 from Thermosynechococcus elongatus.
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Biochemistry,
47,
7304-7316.
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R.Futahashi,
and
H.Fujiwara
(2008).
Identification of stage-specific larval camouflage associated genes in the swallowtail butterfly, Papilio xuthus.
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Dev Genes Evol,
218,
491-504.
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A.Eichinger,
A.Nasreen,
H.J.Kim,
and
A.Skerra
(2007).
Structural insight into the dual ligand specificity and mode of high density lipoprotein association of apolipoprotein D.
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J Biol Chem,
282,
31068-31075.
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PDB codes:
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A.Nasreen,
M.Vogt,
H.J.Kim,
A.Eichinger,
and
A.Skerra
(2006).
Solubility engineering and crystallization of human apolipoprotein D.
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Protein Sci,
15,
190-199.
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C.W.Choi,
K.P.Nam,
D.H.Seo,
J.W.Choi,
C.S.Lee,
H.R.Kim,
and
C.Y.Yun
(2006).
Comparative analysis of two biliproteins, BP1 and BP2, from haemolymph of cabbage white butterfly, Pieris rapae.
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Arch Insect Biochem Physiol,
61,
220-230.
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H.J.Kim,
C.Y.Yun,
Y.S.Han,
I.H.Lee,
Y.J.Kang,
B.R.Jin,
and
S.J.Seo
(2006).
cDNA sequences of two biliproteins, BP1 and BP2, from the cabbage white butterfly, Pieris rapae and their tissue- and stage-specific accumulation.
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Insect Biochem Mol Biol,
36,
54-62.
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Y.Yamada,
K.Nakagawa,
T.Yajima,
K.Saito,
A.Tokushima,
K.Fujiwara,
and
M.Ikeguchi
(2006).
Structural and thermodynamic consequences of removal of a conserved disulfide bond from equine beta-lactoglobulin.
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Proteins,
63,
595-602.
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H.J.Kim,
H.J.Je,
H.M.Cheon,
S.Y.Kong,
J.Han,
C.Y.Yun,
Y.S.Han,
I.H.Lee,
Y.J.Kang,
and
S.J.Seo
(2005).
Accumulation of 23 kDa lipocalin during brain development and injury in Hyphantria cunea.
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Insect Biochem Mol Biol,
35,
1133-1141.
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H.Kayser,
U.Krull-Savage,
and
R.Rilk-van Gessel
(2005).
Developmental profiles of 5-aminolevulinate, porphobilinogen and porphobilinogen synthase activity in Pieris brassicae related to the synthesis of the bilin-binding protein.
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Insect Biochem Mol Biol,
35,
165-174.
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L.W.Schultz,
L.Liu,
M.Cegielski,
and
J.W.Hastings
(2005).
Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole.
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Proc Natl Acad Sci U S A,
102,
1378-1383.
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PDB code:
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M.Allhorn,
A.Klapyta,
and
B.Akerström
(2005).
Redox properties of the lipocalin alpha1-microglobulin: reduction of cytochrome c, hemoglobin, and free iron.
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Free Radic Biol Med,
38,
557-567.
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S.Schlehuber,
and
A.Skerra
(2005).
Anticalins in drug development.
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BioDrugs,
19,
279-288.
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S.Schlehuber,
and
A.Skerra
(2005).
Anticalins as an alternative to antibody technology.
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Expert Opin Biol Ther,
5,
1453-1462.
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S.Vopel,
H.Mühlbach,
and
A.Skerra
(2005).
Rational engineering of a fluorescein-binding anticalin for improved ligand affinity.
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Biol Chem,
386,
1097-1104.
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M.Vogt,
and
A.Skerra
(2004).
Construction of an artificial receptor protein ("anticalin") based on the human apolipoprotein D.
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Chembiochem,
5,
191-199.
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B.Borucki,
H.Otto,
G.Rottwinkel,
J.Hughes,
M.P.Heyn,
and
T.Lamparter
(2003).
Mechanism of Cph1 phytochrome assembly from stopped-flow kinetics and circular dichroism.
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Biochemistry,
42,
13684-13697.
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I.P.Korndörfer,
G.Beste,
and
A.Skerra
(2003).
Crystallographic analysis of an "anticalin" with tailored specificity for fluorescein reveals high structural plasticity of the lipocalin loop region.
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Proteins,
53,
121-129.
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PDB code:
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D.E.Timm,
L.J.Baker,
H.Mueller,
L.Zidek,
and
M.V.Novotny
(2001).
Structural basis of pheromone binding to mouse major urinary protein (MUP-I).
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Protein Sci,
10,
997.
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PDB codes:
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E.J.Gordon,
G.A.Leonard,
S.McSweeney,
and
P.F.Zagalsky
(2001).
The C1 subunit of alpha-crustacyanin: the de novo phasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods.
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Acta Crystallogr D Biol Crystallogr,
57,
1230-1237.
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PDB code:
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L.H.Greene,
E.D.Chrysina,
L.I.Irons,
A.C.Papageorgiou,
K.R.Acharya,
and
K.Brew
(2001).
Role of conserved residues in structure and stability: tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily.
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Protein Sci,
10,
2301-2316.
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PDB codes:
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M.Cianci,
P.J.Rizkallah,
A.Olczak,
J.Raftery,
N.E.Chayen,
P.F.Zagalsky,
and
J.R.Helliwell
(2001).
Structure of lobster apocrustacyanin A1 using softer X-rays.
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Acta Crystallogr D Biol Crystallogr,
57,
1219-1229.
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PDB code:
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A.Skerra
(2000).
Lipocalins as a scaffold.
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Biochim Biophys Acta,
1482,
337-350.
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D.R.Flower,
A.C.North,
and
C.E.Sansom
(2000).
The lipocalin protein family: structural and sequence overview.
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Biochim Biophys Acta,
1482,
9.
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D.R.Flower
(2000).
Experimentally determined lipocalin structures.
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Biochim Biophys Acta,
1482,
46-56.
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G.A.Weiss,
and
H.B.Lowman
(2000).
Anticalins versus antibodies: made-to-order binding proteins for small molecules.
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Chem Biol,
7,
R177-R184.
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O.K.Gasymov,
A.R.Abduragimov,
T.N.Yusifov,
and
B.J.Glasgow
(2000).
Resolution of ligand positions by site-directed tryptophan fluorescence in tear lipocalin.
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Protein Sci,
9,
325-331.
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R.E.Bishop
(2000).
The bacterial lipocalins.
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Biochim Biophys Acta,
1482,
73-83.
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S.Uhrínová,
M.H.Smith,
G.B.Jameson,
D.Uhrín,
L.Sawyer,
and
P.N.Barlow
(2000).
Structural changes accompanying pH-induced dissociation of the beta-lactoglobulin dimer.
|
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Biochemistry,
39,
3565-3574.
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PDB code:
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G.Beste,
F.S.Schmidt,
T.Stibora,
and
A.Skerra
(1999).
Small antibody-like proteins with prescribed ligand specificities derived from the lipocalin fold.
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Proc Natl Acad Sci U S A,
96,
1898-1903.
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A.Weichsel,
J.F.Andersen,
D.E.Champagne,
F.A.Walker,
and
W.R.Montfort
(1998).
Crystal structures of a nitric oxide transport protein from a blood-sucking insect.
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Nat Struct Biol,
5,
304-309.
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PDB codes:
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B.J.Glasgow,
A.R.Abduragimov,
T.N.Yusifov,
O.K.Gasymov,
J.Horwitz,
W.L.Hubbell,
and
K.F.Faull
(1998).
A conserved disulfide motif in human tear lipocalins influences ligand binding.
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Biochemistry,
37,
2215-2225.
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H.Saito
(1998).
Purification and properties of two blue biliproteins from the larval hemolymph and integument of Rhodinia fugax (Lepidoptera: Saturniidae).
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Insect Biochem Mol Biol,
28,
995.
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H.Santa,
J.T.Saarela,
R.Laatikainen,
J.Rautianen,
T.Virtanen,
M.Rytkönen,
and
R.Mäntyjärvi
(1998).
A bovine dander allergen, comparative modeling, and similarities and differences in folding with related proteins.
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J Protein Chem,
17,
657-662.
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J.F.Andersen,
A.Weichsel,
C.A.Balfour,
D.E.Champagne,
and
W.R.Montfort
(1998).
The crystal structure of nitrophorin 4 at 1.5 A resolution: transport of nitric oxide by a lipocalin-based heme protein.
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Structure,
6,
1315-1327.
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PDB code:
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J.J.Lareyre,
M.G.Mattéi,
S.Kasper,
D.E.Ong,
R.J.Matusik,
and
M.C.Orgebin-Crist
(1998).
Genomic organization and chromosomal localization of the murine epididymal retinoic acid-binding protein (mE-RABP) gene.
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Mol Reprod Dev,
50,
387-395.
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R.C.Bugos,
A.D.Hieber,
and
H.Y.Yamamoto
(1998).
Xanthophyll cycle enzymes are members of the lipocalin family, the first identified from plants.
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J Biol Chem,
273,
15321-15324.
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P.Fuentes-Prior,
C.Noeske-Jungblut,
P.Donner,
W.D.Schleuning,
R.Huber,
and
W.Bode
(1997).
Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug.
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Proc Natl Acad Sci U S A,
94,
11845-11850.
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PDB code:
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S.Brownlow,
J.H.Morais Cabral,
R.Cooper,
D.R.Flower,
S.J.Yewdall,
I.Polikarpov,
A.C.North,
and
L.Sawyer
(1997).
Bovine beta-lactoglobulin at 1.8 A resolution--still an enigmatic lipocalin.
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Structure,
5,
481-495.
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PDB code:
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G.Lepperdinger,
B.Strobl,
A.Jilek,
A.Weber,
J.Thalhamer,
H.Flöckner,
and
C.Mollay
(1996).
The lipocalin Xlcpl1 expressed in the neural plate of Xenopus laevis embryos is a secreted retinaldehyde binding protein.
|
| |
Protein Sci,
5,
1250-1260.
|
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G.V.Louie,
P.D.Brownlie,
R.Lambert,
J.B.Cooper,
T.L.Blundell,
S.P.Wood,
V.N.Malashkevich,
A.Hädener,
M.J.Warren,
and
P.M.Shoolingin-Jordan
(1996).
The three-dimensional structure of Escherichia coli porphobilinogen deaminase at 1.76-A resolution.
|
| |
Proteins,
25,
48-78.
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M.A.Bianchet,
G.Bains,
P.Pelosi,
J.Pevsner,
S.H.Snyder,
H.L.Monaco,
and
L.M.Amzel
(1996).
The three-dimensional structure of bovine odorant binding protein and its mechanism of odor recognition.
|
| |
Nat Struct Biol,
3,
934-939.
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PDB code:
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R.E.Bishop,
and
J.H.Weiner
(1996).
"Outlier' lipocalins more than peripheral.
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Trends Biochem Sci,
21,
127.
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D.R.Flower
(1995).
Multiple molecular recognition properties of the lipocalin protein family.
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J Mol Recognit,
8,
185-195.
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R.E.Bishop,
S.S.Penfold,
L.S.Frost,
J.V.Höltje,
and
J.H.Weiner
(1995).
Stationary phase expression of a novel Escherichia coli outer membrane lipoprotein and its relationship with mammalian apolipoprotein D. Implications for the origin of lipocalins.
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| |
J Biol Chem,
270,
23097-23103.
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C.Daffner,
G.Chelvanayagam,
and
P.Argos
(1994).
Structural characteristics and stabilizing principles of bent beta-strands in protein tertiary architectures.
|
| |
Protein Sci,
3,
876-882.
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F.S.Schmidt,
and
A.Skerra
(1994).
The bilin-binding protein of Pieris brassicae. cDNA sequence and regulation of expression reveal distinct features of this insect pigment protein.
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| |
Eur J Biochem,
219,
855-863.
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K.Kock,
C.Ahlers,
and
H.Schmale
(1994).
Structural organization of the genes for rat von Ebner's gland proteins 1 and 2 reveals their close relationship to lipocalins.
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| |
Eur J Biochem,
221,
905-916.
|
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N.N.Alexandrov,
and
N.Go
(1994).
Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins.
|
| |
Protein Sci,
3,
866-875.
|
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|
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P.L.Chau,
and
P.M.Dean
(1994).
Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects.
|
| |
J Comput Aided Mol Des,
8,
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PDB code:
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PDB code:
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Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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