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Hydrolase(o-glycosyl)
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PDB id
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112l
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Contents |
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* Residue conservation analysis
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Enzyme class:
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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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Gene Ontology (GO) functional annotation
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Biological process
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metabolic process
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5 terms
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Biochemical function
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catalytic activity
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4 terms
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DOI no:
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Science
260:1637-1640
(1993)
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PubMed id:
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| |
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Structural basis of amino acid alpha helix propensity.
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M.Blaber,
X.J.Zhang,
B.W.Matthews.
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| |
ABSTRACT
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| |
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The propensity of an amino acid to form an alpha helix in a protein was
determined by multiple amino substitutions at positions 44 and 131 in T4
lysozyme. These positions are solvent-exposed sites within the alpha helices
that comprise, respectively, residues 39 to 50 and 126 to 134. Except for two
acidic substitutions that may be involved in salt bridges, the changes in
stability at the two sites agree well. The stability values also agree with
those observed for corresponding amino acid substitutions in some model
peptides. Thus, helix propensity values derived from model peptides can be
applicable to proteins. Among the 20 naturally occurring amino acids, proline,
glycine, and alanine each have a structurally unique feature that helps to
explain their low or high helix propensities. For the remaining 17 amino acids,
it appears that the side chain hydrophobic surface buried against the side of
the helix contributes substantially to alpha helix propensity.
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Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
E.Babini,
I.Bertini,
V.Borsi,
V.Calderone,
X.Hu,
C.Luchinat,
and
G.Parigi
(2011).
Structural characterization of human S100A16, a low-affinity calcium binder.
|
| |
J Biol Inorg Chem, 16,
243-256.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Lee,
S.I.Blaber,
V.K.Dubey,
and
M.Blaber
(2011).
A polypeptide "building block" for the β-trefoil fold identified by "top-down symmetric deconstruction".
|
| |
J Mol Biol, 407,
744-763.
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|
|
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|
N.Wiradharma,
U.Khoe,
C.A.Hauser,
S.V.Seow,
S.Zhang,
and
Y.Y.Yang
(2011).
Synthetic cationic amphiphilic α-helical peptides as antimicrobial agents.
|
| |
Biomaterials, 32,
2204-2212.
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|
|
S.Beyl,
K.Depil,
A.Hohaus,
A.Stary-Weinzinger,
E.Timin,
W.Shabbir,
M.Kudrnac,
and
S.Hering
(2011).
Physicochemical properties of pore residues predict activation gating of Ca V1.2: a correlation mutation analysis.
|
| |
Pflugers Arch, 461,
53-63.
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|
|
B.G.Ma,
A.Goncearenco,
and
I.N.Berezovsky
(2010).
Thermophilic adaptation of protein complexes inferred from proteomic homology modeling.
|
| |
Structure, 18,
819-828.
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|
|
C.W.am Ende,
H.Y.Meng,
M.Ye,
A.K.Pandey,
and
N.J.Zondlo
(2010).
Design of lanthanide fingers: compact lanthanide-binding metalloproteins.
|
| |
Chembiochem, 11,
1738-1747.
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|
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|
|
F.Shabanpoor,
R.A.Hughes,
S.Zhang,
R.A.Bathgate,
S.Layfield,
M.A.Hossain,
G.W.Tregear,
F.Separovic,
and
J.D.Wade
(2010).
Effect of helix-promoting strategies on the biological activity of novel analogues of the B-chain of INSL3.
|
| |
Amino Acids, 38,
121-131.
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|
|
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|
|
G.Bellesia,
A.I.Jewett,
and
J.E.Shea
(2010).
Sequence periodicity and secondary structure propensity in model proteins.
|
| |
Protein Sci, 19,
141-154.
|
|
|
|
|
|
|
M.L.Tremblay,
A.W.Banks,
and
J.K.Rainey
(2010).
The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment.
|
| |
J Biomol NMR, 46,
257-270.
|
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|
|
|
|
|
M.Miyano,
H.Ago,
H.Saino,
T.Hori,
and
K.Ida
(2010).
Internally bridging water molecule in transmembrane alpha-helical kink.
|
| |
Curr Opin Struct Biol, 20,
456-463.
|
|
|
|
|
|
|
N.Bhattacharjee,
and
P.Biswas
(2010).
Position-specific propensities of amino acids in the β-strand.
|
| |
BMC Struct Biol, 10,
29.
|
|
|
|
|
|
|
N.Bhattacharjee,
and
P.Biswas
(2010).
Statistical analysis and molecular dynamics simulations of ambivalent α-helices.
|
| |
BMC Bioinformatics, 11,
519.
|
|
|
|
|
|
|
S.Chakrapani,
P.Sompornpisut,
P.Intharathep,
B.Roux,
and
E.Perozo
(2010).
The activated state of a sodium channel voltage sensor in a membrane environment.
|
| |
Proc Natl Acad Sci U S A, 107,
5435-5440.
|
|
|
|
|
|
|
C.Yu,
K.P.Mintz,
and
T.Ruiz
(2009).
Investigation of the three-dimensional architecture of the collagen adhesin EmaA of Aggregatibacter actinomycetemcomitans by electron tomography.
|
| |
J Bacteriol, 191,
6253-6261.
|
|
|
|
|
|
|
D.Langosch,
and
I.T.Arkin
(2009).
Interaction and conformational dynamics of membrane-spanning protein helices.
|
| |
Protein Sci, 18,
1343-1358.
|
|
|
|
|
|
|
F.Findeisen,
and
D.L.Minor
(2009).
Disruption of the IS6-AID linker affects voltage-gated calcium channel inactivation and facilitation.
|
| |
J Gen Physiol, 133,
327-343.
|
|
|
|
|
|
|
L.Liu,
Y.Fang,
M.Li,
and
C.Wang
(2009).
Prediction of beta-turn in protein using E-SSpred and support vector machine.
|
| |
Protein J, 28,
175-181.
|
|
|
|
|
|
|
M.Castillo,
J.Mulet,
M.Aldea,
S.Gerber,
S.Sala,
F.Sala,
and
M.Criado
(2009).
Role of the N-terminal alpha-helix in biogenesis of alpha7 nicotinic receptors.
|
| |
J Neurochem, 108,
1399-1409.
|
|
|
|
|
|
|
S.Laroche-Pierre,
J.Jodoin,
and
A.C.LeBlanc
(2009).
Helix 3 is necessary and sufficient for prion protein's anti-Bax function.
|
| |
J Neurochem, 108,
1019-1031.
|
|
|
|
|
|
|
A.J.Labro,
A.L.Raes,
A.Grottesi,
D.Van Hoorick,
M.S.Sansom,
and
D.J.Snyders
(2008).
Kv channel gating requires a compatible S4-S5 linker and bottom part of S6, constrained by non-interacting residues.
|
| |
J Gen Physiol, 132,
667-680.
|
|
|
|
|
|
|
F.Rodriguez,
F.Arsène-Ploetze,
W.Rist,
S.Rüdiger,
J.Schneider-Mergener,
M.P.Mayer,
and
B.Bukau
(2008).
Molecular basis for regulation of the heat shock transcription factor sigma32 by the DnaK and DnaJ chaperones.
|
| |
Mol Cell, 32,
347-358.
|
|
|
|
|
|
|
K.Yura,
and
M.Go
(2008).
Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles.
|
| |
BMC Plant Biol, 8,
79.
|
|
|
|
|
|
|
M.Duan,
M.Huang,
C.Ma,
L.Li,
and
Y.Zhou
(2008).
Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures.
|
| |
Protein Sci, 17,
1505-1512.
|
|
|
|
|
|
|
S.Chakrapani,
L.G.Cuello,
D.M.Cortes,
and
E.Perozo
(2008).
Structural dynamics of an isolated voltage-sensor domain in a lipid bilayer.
|
| |
Structure, 16,
398-409.
|
|
|
|
|
|
|
F.Avbelj,
and
S.G.Grdadolnik
(2007).
Electrostatic screening and backbone preferences of amino acid residues in urea-denatured ubiquitin.
|
| |
Protein Sci, 16,
273-284.
|
|
|
|
|
|
|
K.A.Scott,
D.O.Alonso,
S.Sato,
A.R.Fersht,
and
V.Daggett
(2007).
Conformational entropy of alanine versus glycine in protein denatured states.
|
| |
Proc Natl Acad Sci U S A, 104,
2661-2666.
|
|
|
|
|
|
|
K.Bakshi,
R.W.Mercier,
and
S.Pavlopoulos
(2007).
Interaction of a fragment of the cannabinoid CB1 receptor C-terminus with arrestin-2.
|
| |
FEBS Lett, 581,
5009-5016.
|
|
|
|
|
|
|
M.Araki,
and
A.Tamura
(2007).
Transformation of an alpha-helix peptide into a beta-hairpin induced by addition of a fragment results in creation of a coexisting state.
|
| |
Proteins, 66,
860-868.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.Tuller,
B.Chor,
and
N.Nelson
(2007).
Forbidden penta-peptides.
|
| |
Protein Sci, 16,
2251-2259.
|
|
|
|
|
|
|
X.Wang,
L.Du,
and
B.Z.Peterson
(2007).
Calcicludine binding to the outer pore of L-type calcium channels is allosterically coupled to dihydropyridine binding.
|
| |
Biochemistry, 46,
7590-7598.
|
|
|
|
|
|
|
A.C.Hausrath
(2006).
A model for the coupling of alpha-helix and tertiary contact formation.
|
| |
Protein Sci, 15,
2051-2061.
|
|
|
|
|
|
|
H.Chen,
F.Gu,
and
Z.Huang
(2006).
Improved Chou-Fasman method for protein secondary structure prediction.
|
| |
BMC Bioinformatics, 7,
S14.
|
|
|
|
|
|
|
J.López-Llano,
L.A.Campos,
and
J.Sancho
(2006).
Alpha-helix stabilization by alanine relative to glycine: roles of polar and apolar solvent exposures and of backbone entropy.
|
| |
Proteins, 64,
769-778.
|
|
|
|
|
|
|
J.S.Fetrow,
S.T.Knutson,
and
M.H.Edgell
(2006).
Mutations in alpha-helical solvent-exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations.
|
| |
Proteins, 63,
356-372.
|
|
|
|
|
|
|
T.P.Creamer,
J.S.Fetrow,
and
G.Rose
(2006).
Rose is a rose is a rose. Especially if you're a George.
|
| |
Proteins, 63,
268-272.
|
|
|
|
|
|
|
W.Xian,
P.J.Connolly,
M.Oslin,
A.C.Hausrath,
and
J.J.Osterhout
(2006).
Fundamental processes of protein folding: measuring the energetic balance between helix formation and hydrophobic interactions.
|
| |
Protein Sci, 15,
2062-2070.
|
|
|
|
|
|
|
J.A.Kritzer,
J.Tirado-Rives,
S.A.Hart,
J.D.Lear,
W.L.Jorgensen,
and
A.Schepartz
(2005).
Relationship between side chain structure and 14-helix stability of beta3-peptides in water.
|
| |
J Am Chem Soc, 127,
167-178.
|
|
|
|
|
|
|
O.E.Acevedo,
and
L.R.Lareo
(2005).
Amino acid propensities revisited.
|
| |
OMICS, 9,
391-399.
|
|
|
|
|
|
|
S.Choe,
and
S.X.Sun
(2005).
The elasticity of alpha-helices.
|
| |
J Chem Phys, 122,
244912.
|
|
|
|
|
|
|
V.V.Loladze,
and
G.I.Makhatadze
(2005).
Both helical propensity and side-chain hydrophobicity at a partially exposed site in alpha-helix contribute to the thermodynamic stability of ubiquitin.
|
| |
Proteins, 58,
1-6.
|
|
|
|
|
|
|
A.Paiardini,
F.Bossa,
and
S.Pascarella
(2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
|
| |
Protein Sci, 13,
2992-3005.
|
|
|
|
|
|
|
M.M.He,
Z.A.Wood,
W.A.Baase,
H.Xiao,
and
B.W.Matthews
(2004).
Alanine-scanning mutagenesis of the beta-sheet region of phage T4 lysozyme suggests that tertiary context has a dominant effect on beta-sheet formation.
|
| |
Protein Sci, 13,
2716-2724.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
O.Keskin,
D.Yuret,
A.Gursoy,
M.Turkay,
and
B.Erman
(2004).
Relationships between amino acid sequence and backbone torsion angle preferences.
|
| |
Proteins, 55,
992-998.
|
|
|
|
|
|
|
R.Lu,
A.Limón,
E.Devroe,
P.A.Silver,
P.Cherepanov,
and
A.Engelman
(2004).
Class II integrase mutants with changes in putative nuclear localization signals are primarily blocked at a postnuclear entry step of human immunodeficiency virus type 1 replication.
|
| |
J Virol, 78,
12735-12746.
|
|
|
|
|
|
|
D.L.Lee,
S.Ivaninskii,
P.Burkhard,
and
R.S.Hodges
(2003).
Unique stabilizing interactions identified in the two-stranded alpha-helical coiled-coil: crystal structure of a cortexillin I/GCN4 hybrid coiled-coil peptide.
|
| |
Protein Sci, 12,
1395-1405.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.N.Ermolenko,
J.M.Richardson,
and
G.I.Makhatadze
(2003).
Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity.
|
| |
Protein Sci, 12,
1169-1176.
|
|
|
|
|
|
|
D.H.Hackos,
T.H.Chang,
and
K.J.Swartz
(2002).
Scanning the intracellular S6 activation gate in the shaker K+ channel.
|
| |
J Gen Physiol, 119,
521-532.
|
|
|
|
|
|
|
D.Shortle
(2002).
Composites of local structure propensities: evidence for local encoding of long-range structure.
|
| |
Protein Sci, 11,
18-26.
|
|
|
|
|
|
|
H.Zhou,
and
Y.Zhou
(2002).
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments.
|
| |
Proteins, 49,
483-492.
|
|
|
|
|
|
|
K.L.Lou,
P.T.Huang,
Y.S.Shiau,
and
Y.Y.Shiau
(2002).
Molecular determinants of the hanatoxin binding in voltage-gated K+-channel drk1.
|
| |
J Mol Recognit, 15,
175-179.
|
|
|
|
|
|
|
M.Petukhov,
K.Uegaki,
N.Yumoto,
and
L.Serrano
(2002).
Amino acid intrinsic alpha-helical propensities III: positional dependence at several positions of C terminus.
|
| |
Protein Sci, 11,
766-777.
|
|
|
|
|
|
|
D.Krowarsch,
and
J.Otlewski
(2001).
Amino-acid substitutions at the fully exposed P1 site of bovine pancreatic trypsin inhibitor affect its stability.
|
| |
Protein Sci, 10,
715-724.
|
|
|
|
|
|
|
M.N.Tamashiro,
and
P.Pincus
(2001).
Helix-coil transition in homopolypeptides under stretching.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys, 63,
021909.
|
|
|
|
|
|
|
S.T.Thomas,
V.V.Loladze,
and
G.I.Makhatadze
(2001).
Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of alpha-helices.
|
| |
Proc Natl Acad Sci U S A, 98,
10670-10675.
|
|
|
|
|
|
|
S.V.Taylor,
P.Kast,
and
D.Hilvert
(2001).
Investigating and Engineering Enzymes by Genetic Selection.
|
| |
Angew Chem Int Ed Engl, 40,
3310-3335.
|
|
|
|
|
|
|
Y.Li-Smerin,
and
K.J.Swartz
(2001).
Helical structure of the COOH terminus of S3 and its contribution to the gating modifier toxin receptor in voltage-gated ion channels.
|
| |
J Gen Physiol, 117,
205-218.
|
|
|
|
|
|
|
B.S.Jin,
J.R.Ryu,
K.Ahn,
and
Y.G.Yu
(2000).
Design of a peptide inhibitor that blocks the cell fusion mediated by glycoprotein 41 of human immunodeficiency virus type 1.
|
| |
AIDS Res Hum Retroviruses, 16,
1797-1804.
|
|
|
|
|
|
|
C.Krittanai,
and
W.C.Johnson
(2000).
The relative order of helical propensity of amino acids changes with solvent environment.
|
| |
Proteins, 39,
132-141.
|
|
|
|
|
|
|
J.M.Word,
R.C.Bateman,
B.K.Presley,
S.C.Lovell,
and
D.C.Richardson
(2000).
Exploring steric constraints on protein mutations using MAGE/PROBE.
|
| |
Protein Sci, 9,
2251-2259.
|
|
|
|
|
|
|
M.A.Weiss,
Q.X.Hua,
W.Jia,
Y.C.Chu,
R.Y.Wang,
and
P.G.Katsoyannis
(2000).
Hierarchical protein "un-design": insulin's intrachain disulfide bridge tethers a recognition alpha-helix.
|
| |
Biochemistry, 39,
15429-15440.
|
|
|
|
|
|
|
M.M.Wuebbens,
M.T.Liu,
K.Rajagopalan,
and
H.Schindelin
(2000).
Insights into molybdenum cofactor deficiency provided by the crystal structure of the molybdenum cofactor biosynthesis protein MoaC.
|
| |
Structure, 8,
709-718.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Strop,
A.M.Marinescu,
and
S.L.Mayo
(2000).
Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design.
|
| |
Protein Sci, 9,
1391-1394.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
X.Zhou,
F.Alber,
G.Folkers,
G.H.Gonnet,
and
G.Chelvanayagam
(2000).
An analysis of the helix-to-strand transition between peptides with identical sequence.
|
| |
Proteins, 41,
248-256.
|
|
|
|
|
|
|
A.Chakrabarti,
S.Srivastava,
C.P.Swaminathan,
A.Surolia,
and
R.Varadarajan
(1999).
Thermodynamics of replacing an alpha-helical Pro residue in the P40S mutant of Escherichia coli thioredoxin.
|
| |
Protein Sci, 8,
2455-2459.
|
|
|
|
|
|
|
B.M.Brown,
and
R.T.Sauer
(1999).
Tolerance of Arc repressor to multiple-alanine substitutions.
|
| |
Proc Natl Acad Sci U S A, 96,
1983-1988.
|
|
|
|
|
|
|
C.A.Rohl,
W.Fiori,
and
R.L.Baldwin
(1999).
Alanine is helix-stabilizing in both template-nucleated and standard peptide helices.
|
| |
Proc Natl Acad Sci U S A, 96,
3682-3687.
|
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Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme.
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Protein Sci, 3,
1031-1039.
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PDB codes:
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Y.Bai,
and
S.W.Englander
(1994).
Hydrogen bond strength and beta-sheet propensities: the role of a side chain blocking effect.
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Proteins, 18,
262-266.
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P.Pjura,
and
B.W.Matthews
(1993).
Structures of randomly generated mutants of T4 lysozyme show that protein stability can be enhanced by relaxation of strain and by improved hydrogen bonding via bound solvent.
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Protein Sci, 2,
2226-2232.
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PDB codes:
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T.V.Borchert,
R.Abagyan,
K.V.Kishan,
J.P.Zeelen,
and
R.K.Wierenga
(1993).
The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop.
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Structure, 1,
205-213.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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
