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PDBsum entry 1abf
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Binding protein
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PDB id
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1abf
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Contents |
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* Residue conservation analysis
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Nature
340:404-407
(1989)
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PubMed id:
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Substrate specificity and affinity of a protein modulated by bound water molecules.
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F.A.Quiocho,
D.K.Wilson,
N.K.Vyas.
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ABSTRACT
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Water molecules influence molecular interactions in all biological systems, yet
it is extremely difficult to understand their effects in precise atomic detail.
Here we present evidence, based on highly refined atomic structures of the
complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and
D-galactose, that bound water molecules, coupled with localized conformational
changes, can govern substrate specificity and affinity. The atoms common to the
three sugars are identically positioned in the binding site and the same nine
strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded
water molecules in the site contribute further to tight binding of L-arabinose
but create an unfavourable interaction with the methyl group of D-fucose.
Equally tight binding of D-galactose is attained by the replacement of one of
the hydrogen-bonded water molecules by its--CH2OH group, coordinated with
localized structural changes which include a shift and redirection of the
hydrogen-bonding interactions of the other water molecule. These observations
illustrate how ordered water molecules can contribute directly to the properties
of proteins by influencing their interaction with ligands.
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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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D.J.Huggins,
G.J.McKenzie,
D.D.Robinson,
A.J.Narváez,
B.Hardwick,
M.Roberts-Thomson,
A.R.Venkitaraman,
G.H.Grant,
and
M.C.Payne
(2010).
Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation.
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PLoS Comput Biol,
6,
0.
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A.Szumna
(2009).
Water co-encapsulation in an inverted molecular capsule.
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Chem Commun (Camb),
(),
4191-4193.
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B.Schreier,
C.Stumpp,
S.Wiesner,
and
B.Höcker
(2009).
Computational design of ligand binding is not a solved problem.
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Proc Natl Acad Sci U S A,
106,
18491-18496.
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PDB code:
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D.A.Kuntz,
W.Zhong,
J.Guo,
D.R.Rose,
and
G.J.Boons
(2009).
The Molecular Basis of Inhibition of Golgi alpha-Mannosidase II by Mannostatin A.
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Chembiochem,
10,
268-277.
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PDB codes:
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M.Mazik,
A.Hartmann,
and
P.G.Jones
(2009).
Highly effective recognition of carbohydrates by phenanthroline-based receptors: alpha- versus beta-anomer binding preference.
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Chemistry,
15,
9147-9159.
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P.C.Kohler,
T.Ritschel,
W.B.Schweizer,
G.Klebe,
and
F.Diederich
(2009).
High-affinity inhibitors of tRNA-guanine transglycosylase replacing the function of a structural water cluster.
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Chemistry,
15,
10809-10817.
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A.D.Hill,
and
P.J.Reilly
(2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
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J Comput Chem,
29,
1131-1141.
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S.Chopra,
R.M.Dooling,
C.G.Horner,
and
E.E.Howell
(2008).
A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase.
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J Biol Chem,
283,
4690-4698.
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A.C.Dumetz,
A.M.Snellinger-O'brien,
E.W.Kaler,
and
A.M.Lenhoff
(2007).
Patterns of protein protein interactions in salt solutions and implications for protein crystallization.
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Protein Sci,
16,
1867-1877.
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C.A.MacRaild,
A.H.Daranas,
A.Bronowska,
and
S.W.Homans
(2007).
Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein.
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J Mol Biol,
368,
822-832.
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Z.Li,
and
T.Lazaridis
(2007).
Water at biomolecular binding interfaces.
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Phys Chem Chem Phys,
9,
573-581.
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K.Stierand,
P.C.Maass,
and
M.Rarey
(2006).
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams.
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Bioinformatics,
22,
1710-1716.
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M.Renatus,
S.G.Parrado,
A.D'Arcy,
U.Eidhoff,
B.Gerhartz,
U.Hassiepen,
B.Pierrat,
R.Riedl,
D.Vinzenz,
S.Worpenberg,
and
M.Kroemer
(2006).
Structural basis of ubiquitin recognition by the deubiquitinating protease USP2.
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Structure,
14,
1293-1302.
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PDB code:
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A.E.Cho,
V.Guallar,
B.J.Berne,
and
R.Friesner
(2005).
Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach.
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J Comput Chem,
26,
915-931.
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M.Sobhany,
J.Dong,
and
M.Negishi
(2005).
Two-step mechanism that determines the donor binding specificity of human UDP-N-acetylhexosaminyltransferase.
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J Biol Chem,
280,
23441-23445.
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B.Jayaram,
and
T.Jain
(2004).
The role of water in protein-DNA recognition.
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Annu Rev Biophys Biomol Struct,
33,
343-361.
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N.K.Karpowich,
H.H.Huang,
P.C.Smith,
and
J.F.Hunt
(2003).
Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding.
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J Biol Chem,
278,
8429-8434.
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PDB codes:
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Q.Vicens,
and
E.Westhof
(2003).
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures.
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Biopolymers,
70,
42-57.
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H.I.Jung,
S.J.Bowden,
A.Cooper,
and
R.N.Perham
(2002).
Thermodynamic analysis of the binding of component enzymes in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
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Protein Sci,
11,
1091-1100.
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M.Goel,
D.Jain,
K.J.Kaur,
R.Kenoth,
B.G.Maiya,
M.J.Swamy,
and
D.M.Salunke
(2001).
Functional equality in the absence of structural similarity: an added dimension to molecular mimicry.
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J Biol Chem,
276,
39277-39281.
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PDB code:
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C.E.Liu,
P.Q.Liu,
A.Wolf,
E.Lin,
and
G.F.Ames
(1999).
Both lobes of the soluble receptor of the periplasmic histidine permease, an ABC transporter (traffic ATPase), interact with the membrane-bound complex. Effect of different ligands and consequences for the mechanism of action.
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J Biol Chem,
274,
739-747.
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D.Ringe,
and
C.Mattos
(1999).
Analysis of the binding surfaces of proteins.
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Med Res Rev,
19,
321-331.
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J.A.Cuff,
and
G.J.Barton
(1999).
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
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Proteins,
34,
508-519.
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J.Bouckaert,
T.W.Hamelryck,
L.Wyns,
and
R.Loris
(1999).
The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A.
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J Biol Chem,
274,
29188-29195.
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PDB codes:
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R.Ravishankar,
K.Suguna,
A.Surolia,
and
M.Vijayan
(1999).
Structures of the complexes of peanut lectin with methyl-beta-galactose and N-acetyllactosamine and a comparative study of carbohydrate binding in Gal/GalNAc-specific legume lectins.
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Acta Crystallogr D Biol Crystallogr,
55,
1375-1382.
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PDB codes:
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D.G.Vassylyev,
H.Tomitori,
K.Kashiwagi,
K.Morikawa,
and
K.Igarashi
(1998).
Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity.
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J Biol Chem,
273,
17604-17609.
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PDB code:
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M.Gregoriou,
M.E.Noble,
K.A.Watson,
E.F.Garman,
T.M.Krulle,
C.de la Fuente,
G.W.Fleet,
N.G.Oikonomakos,
and
L.N.Johnson
(1998).
The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding.
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Protein Sci,
7,
915-927.
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PDB codes:
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F.A.Quiocho,
J.C.Spurlino,
and
L.E.Rodseth
(1997).
Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor.
|
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Structure,
5,
997.
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PDB codes:
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L.J.Martins,
C.P.Hill,
and
W.R.Ellis
(1997).
Structures of wild-type chloromet and L103N hydroxomet Themiste zostericola myohemerythrins at 1.8 A resolution.
|
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Biochemistry,
36,
7044-7049.
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PDB codes:
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M.A.Schumacher,
A.Glasfeld,
H.Zalkin,
and
R.G.Brennan
(1997).
The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.
|
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J Biol Chem,
272,
22648-22653.
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PDB code:
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A.Wolf,
K.C.Lee,
J.F.Kirsch,
and
G.F.Ames
(1996).
Ligand-dependent conformational plasticity of the periplasmic histidine-binding protein HisJ. Involvement in transport specificity.
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J Biol Chem,
271,
21243-21250.
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F.A.Quiocho,
and
P.S.Ledvina
(1996).
Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes.
|
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Mol Microbiol,
20,
17-25.
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J.E.Ladbury
(1996).
Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design.
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Chem Biol,
3,
973-980.
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J.R.Tame,
S.H.Sleigh,
A.J.Wilkinson,
and
J.E.Ladbury
(1996).
The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.
|
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Nat Struct Biol,
3,
998.
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PDB codes:
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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.
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Biosci Rep,
16,
1.
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S.Paul
(1996).
Natural catalytic antibodies.
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Mol Biotechnol,
5,
197-207.
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W.E.Royer,
A.Pardanani,
Q.H.Gibson,
E.S.Peterson,
and
J.M.Friedman
(1996).
Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin.
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Proc Natl Acad Sci U S A,
93,
14526-14531.
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C.S.Poornima,
and
P.M.Dean
(1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.
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J Comput Aided Mol Des,
9,
500-512.
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C.S.Poornima,
and
P.M.Dean
(1995).
Hydration in drug design. 2. Influence of local site surface shape on water binding.
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J Comput Aided Mol Des,
9,
513-520.
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J.R.Cupp-Vickery,
and
T.L.Poulos
(1995).
Structure of cytochrome P450eryF involved in erythromycin biosynthesis.
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Nat Struct Biol,
2,
144-153.
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PDB code:
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K.Huang,
W.Lu,
S.Anderson,
M.Laskowski,
and
M.N.James
(1995).
Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B.
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Protein Sci,
4,
1985-1997.
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PDB codes:
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V.Helms,
and
R.C.Wade
(1995).
Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.
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Biophys J,
69,
810-824.
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G.Hummer,
and
D.M.Soumpasis
(1994).
Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for B-DNA.
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Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics,
50,
5085-5095.
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M.Peräkylä,
and
T.A.Pakkanen
(1994).
Quantum mechanical model assembly study on the energetics of binding of arabinose, fucose, and galactose to L-arabinose-binding protein.
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Proteins,
20,
367-372.
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M.Potts
(1994).
Desiccation tolerance of prokaryotes.
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Microbiol Rev,
58,
755-805.
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T.L.Lowary,
S.J.Swiedler,
and
O.Hindsgaul
(1994).
Recognition of synthetic analogues of the acceptor, beta-D-Gal p-OR, by the blood-group H gene-specified glycosyltransferase.
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Carbohydr Res,
256,
257-273.
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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.
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Proc Natl Acad Sci U S A,
91,
1089-1093.
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PDB codes:
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K.Warncke,
and
P.L.Dutton
(1993).
Experimental resolution of the free energies of aqueous solvation contributions to ligand-protein binding: quinone-QA site interactions in the photosynthetic reaction center protein.
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Proc Natl Acad Sci U S A,
90,
2920-2924.
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S.H.Rotstein,
and
M.A.Murcko
(1993).
GenStar: a method for de novo drug design.
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J Comput Aided Mol Des,
7,
23-43.
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T.L.Lowary,
and
O.Hindsgaul
(1993).
Recognition of synthetic deoxy and deoxyfluoro analogs of the acceptor alpha-L-Fuc p-(1-->2)-beta-D-Gal p-OR by the blood-group A and B gene-specified glycosyltransferases.
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Carbohydr Res,
249,
163-195.
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A.Perczel,
B.M.Foxman,
and
G.D.Fasman
(1992).
How reverse turns may mediate the formation of helical segments in proteins: an x-ray model.
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Proc Natl Acad Sci U S A,
89,
8210-8214.
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J.S.Finer-Moore,
A.A.Kossiakoff,
J.H.Hurley,
T.Earnest,
and
R.M.Stroud
(1992).
Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.
|
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Proteins,
12,
203-222.
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PDB code:
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K.Peek,
S.A.Wilson,
M.Prescott,
and
R.M.Daniel
(1992).
Some characteristics of a serine proteinase isolated from an extreme thermophile for use in kinetically controlled peptide bond synthesis.
|
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Ann N Y Acad Sci,
672,
471-477.
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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
code is
shown on the right.
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Links
