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PDBsum entry 1k6f
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Structural protein
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PDB id
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1k6f
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PDB id:
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Structural protein
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Title:
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Crystal structure of the collagen triple helix model [(pro-pro-gly) 10]3
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Structure:
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Collagen triple helix. Chain: a, b, c, d, e, f. Engineered: yes
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Source:
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Synthetic: yes. Other_details: the protein was chemically synthesized.
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Biol. unit:
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Trimer (from
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Resolution:
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1.30Å
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R-factor:
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0.226
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R-free:
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0.297
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Authors:
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R.Berisio,L.Vitagliano,L.Mazzarella,A.Zagari
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Key ref:
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R.Berisio
et al.
(2002).
Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3).
Protein Sci,
11,
262-270.
PubMed id:
DOI:
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Date:
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16-Oct-01
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Release date:
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30-Jan-02
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PROCHECK
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Headers
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References
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Q80BK4
(Q80BK4_SHV2) -
Saimiri transformation-associated protein from Saimiriine herpesvirus 2
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Seq:
Struc:
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99 a.a.
29 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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DOI no:
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Protein Sci
11:262-270
(2002)
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PubMed id:
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Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3).
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R.Berisio,
L.Vitagliano,
L.Mazzarella,
A.Zagari.
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ABSTRACT
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The first report of the full-length structure of the collagen-like polypeptide
[(Pro-Pro-Gly)(10)](3) is given. This structure was obtained from crystals grown
in a microgravity environment, which diffracted up to 1.3 A, using synchrotron
radiation. The final model, which was refined to an R(factor) of 0.18, is the
highest-resolution description of a collagen triple helix reported to date. This
structure provides clues regarding a series of aspects related to collagen
triple helix structure and assembly. The strict dependence of proline puckering
on the position inside the Pro-Pro-Gly triplets and the correlation between
backbone and side chain dihedral angles support the propensity-based mechanism
of triple helix stabilization/destabilization induced by hydroxyproline.
Furthermore, the analysis of [(Pro-Pro-Gly)(10)](3) packing, which is governed
by electrostatic interactions, suggests that charges may act as locking features
in the axial organization of triple helices in the collagen fibrils.
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Selected figure(s)
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Figure 1.
Fig. 1. (A) Organization of the [(Pro-Pro-Gly)[10][3]
triple helices in the ac plane. Chains are colored with a
ramping code from blue (N-termini) to red (C-termini). The two
molecules in the asymmetric unit are the top-center (molecule 1)
and the bottom-center (molecule 2) molecules. (B) Average model
obtained in the subcell approximation (Vitagliano et al. 2001a)
in the ac` plane. The c` corresponds to a ninth of the
full-length c axis. (C) Electron density map (2Fo-Fc), extended
to the whole unit cell, contoured at 2.0  . (D) Omit
map (Fo-Fc) of a representative triplet contoured at 3.5 .
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Figure 3.
Fig. 3. Distribution of water molecules as a function of
their distance from the nearest protein atom.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2002,
11,
262-270)
copyright 2002.
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Figures were
selected
by an automated process.
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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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A.Tuer,
S.Krouglov,
R.Cisek,
D.Tokarz,
and
V.Barzda
(2011).
Three-dimensional visualization of the first hyperpolarizability tensor.
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J Comput Chem,
32,
1128-1134.
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T.Suehiro,
T.Tada,
T.Waku,
N.Tanaka,
C.Hongo,
S.Yamamoto,
A.Nakahira,
and
C.Kojima
(2011).
Temperature-dependent higher order structures of the (Pro-Pro-Gly)(10) -modified dendrimer.
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Biopolymers,
95,
270-277.
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J.A.Fallas,
L.E.O'Leary,
and
J.D.Hartgerink
(2010).
Synthetic collagen mimics: self-assembly of homotrimers, heterotrimers and higher order structures.
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Chem Soc Rev,
39,
3510-3527.
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K.Okuyama,
T.Morimoto,
H.Narita,
T.Kawaguchi,
K.Mizuno,
H.P.Bächinger,
G.Wu,
and
K.Noguchi
(2010).
Two crystal modifications of (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices.
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Acta Crystallogr D Biol Crystallogr,
66,
88-96.
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PDB codes:
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M.D.Shoulders,
K.A.Satyshur,
K.T.Forest,
and
R.T.Raines
(2010).
Stereoelectronic and steric effects in side chains preorganize a protein main chain.
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Proc Natl Acad Sci U S A,
107,
559-564.
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PDB code:
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V.Nucciotti,
C.Stringari,
L.Sacconi,
F.Vanzi,
L.Fusi,
M.Linari,
G.Piazzesi,
V.Lombardi,
and
F.S.Pavone
(2010).
Probing myosin structural conformation in vivo by second-harmonic generation microscopy.
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Proc Natl Acad Sci U S A,
107,
7763-7768.
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J.A.Fallas,
V.Gauba,
and
J.D.Hartgerink
(2009).
Solution structure of an ABC collagen heterotrimer reveals a single-register helix stabilized by electrostatic interactions.
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J Biol Chem,
284,
26851-26859.
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PDB code:
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K.Okuyama,
C.Hongo,
G.Wu,
K.Mizuno,
K.Noguchi,
S.Ebisuzaki,
Y.Tanaka,
N.Nishino,
and
H.P.Bächinger
(2009).
High-resolution structures of collagen-like peptides [(Pro-Pro-Gly)(4)-Xaa-Yaa-Gly-(Pro-Pro-Gly)(4)]: Implications for triple-helix hydration and Hyp(X) puckering.
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Biopolymers,
91,
361-372.
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PDB codes:
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L.M.Haupert,
and
G.J.Simpson
(2009).
Chirality in nonlinear optics.
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Annu Rev Phys Chem,
60,
345-365.
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M.D.Shoulders,
and
R.T.Raines
(2009).
Collagen structure and stability.
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Annu Rev Biochem,
78,
929-958.
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S.T.Philominathan,
T.Koide,
K.Hamada,
H.Yasui,
S.Seifert,
O.Matsushita,
and
J.Sakon
(2009).
Unidirectional binding of clostridial collagenase to triple helical substrates.
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J Biol Chem,
284,
10868-10876.
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Y.Li,
B.Brodsky,
and
J.Baum
(2009).
NMR conformational and dynamic consequences of a gly to ser substitution in an osteogenesis imperfecta collagen model peptide.
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J Biol Chem,
284,
20660-20667.
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K.M.Ravikumar,
and
W.Hwang
(2008).
Region-specific role of water in collagen unwinding and assembly.
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Proteins,
72,
1320-1332.
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G.D.Fullerton,
and
A.Rahal
(2007).
Collagen structure: the molecular source of the tendon magic angle effect.
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J Magn Reson Imaging,
25,
345-361.
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K.Okuyama,
H.Narita,
T.Kawaguchi,
K.Noguchi,
Y.Tanaka,
and
N.Nishino
(2007).
Unique side chain conformation of a Leu residue in a triple-helical structure.
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Biopolymers,
86,
212-221.
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PDB codes:
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M.A.Bryan,
J.W.Brauner,
G.Anderle,
C.R.Flach,
B.Brodsky,
and
R.Mendelsohn
(2007).
FTIR studies of collagen model peptides: complementary experimental and simulation approaches to conformation and unfolding.
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J Am Chem Soc,
129,
7877-7884.
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K.Okuyama,
G.Wu,
N.Jiravanichanun,
C.Hongo,
and
K.Noguchi
(2006).
Helical twists of collagen model peptides.
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Biopolymers,
84,
421-432.
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K.Okuyama,
X.Xu,
M.Iguchi,
and
K.Noguchi
(2006).
Revision of collagen molecular structure.
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Biopolymers,
84,
181-191.
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N.Jiravanichanun,
N.Nishino,
and
K.Okuyama
(2006).
Conformation of alloHyp in the Y position in the host-guest peptide with the pro-pro-gly sequence: implication of the destabilization of (Pro-alloHyp-Gly)10.
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Biopolymers,
81,
225-233.
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U.Kusebauch,
S.A.Cadamuro,
H.J.Musiol,
M.O.Lenz,
J.Wachtveitl,
L.Moroder,
and
C.Renner
(2006).
Photocontrolled folding and unfolding of a collagen triple helix.
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Angew Chem Int Ed Engl,
45,
7015-7018.
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A.E.Aliev
(2005).
Solid-state NMR studies of collagen-based parchments and gelatin.
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Biopolymers,
77,
230-245.
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C.L.Jenkins,
A.I.McCloskey,
I.A.Guzei,
E.S.Eberhardt,
and
R.T.Raines
(2005).
O-acylation of hydroxyproline residues: effect on peptide-bond isomerization and collagen stability.
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Biopolymers,
80,
1-8.
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R.Willaert,
I.Zegers,
L.Wyns,
and
M.Sleutel
(2005).
Protein crystallization in hydrogel beads.
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Acta Crystallogr D Biol Crystallogr,
61,
1280-1288.
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S.Vesentini,
C.F.Fitié,
F.M.Montevecchi,
and
A.Redaelli
(2005).
Molecular assessment of the elastic properties of collagen-like homotrimer sequences.
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Biomech Model Mechanobiol,
3,
224-234.
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D.Barth,
A.G.Milbradt,
C.Renner,
and
L.Moroder
(2004).
A (4R)- or a (4S)-fluoroproline residue in position Xaa of the (Xaa-Yaa-Gly) collagen repeat severely affects triple-helix formation.
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Chembiochem,
5,
79-86.
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J.P.Malone,
A.George,
and
A.Veis
(2004).
Type I collagen N-telopeptides adopt an ordered structure when docked to their helix receptor during fibrillogenesis.
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Proteins,
54,
206-215.
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K.Okuyama,
C.Hongo,
R.Fukushima,
G.Wu,
H.Narita,
K.Noguchi,
Y.Tanaka,
and
N.Nishino
(2004).
Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering.
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Biopolymers,
76,
367-377.
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PDB codes:
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R.Berisio,
V.Granata,
L.Vitagliano,
and
A.Zagari
(2004).
Characterization of collagen-like heterotrimers: implications for triple-helix stability.
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Biopolymers,
73,
682-688.
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A.E.Miele,
L.Federici,
G.Sciara,
F.Draghi,
M.Brunori,
and
B.Vallone
(2003).
Analysis of the effect of microgravity on protein crystal quality: the case of a myoglobin triple mutant.
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Acta Crystallogr D Biol Crystallogr,
59,
982-988.
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PDB codes:
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H.Feinberg,
J.C.Uitdehaag,
J.M.Davies,
R.Wallis,
K.Drickamer,
and
W.I.Weis
(2003).
Crystal structure of the CUB1-EGF-CUB2 region of mannose-binding protein associated serine protease-2.
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EMBO J,
22,
2348-2359.
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PDB code:
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J.Slager,
and
A.J.Domb
(2003).
Biopolymer stereocomplexes.
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Adv Drug Deliv Rev,
55,
549-583.
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J.Stetefeld,
S.Frank,
M.Jenny,
T.Schulthess,
R.A.Kammerer,
S.Boudko,
R.Landwehr,
K.Okuyama,
and
J.Engel
(2003).
Collagen stabilization at atomic level: crystal structure of designed (GlyProPro)10foldon.
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Structure,
11,
339-346.
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PDB code:
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K.V.Simon-Lukasik,
A.V.Persikov,
B.Brodsky,
J.A.Ramshaw,
W.R.Laws,
J.B.Alexander Ross,
and
R.D.Ludescher
(2003).
Fluorescence determination of tryptophan side-chain accessibility and dynamics in triple-helical collagen-like peptides.
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Biophys J,
84,
501-508.
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J.K.Rainey,
and
M.C.Goh
(2002).
A statistically derived parameterization for the collagen triple-helix.
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Protein Sci,
11,
2748-2754.
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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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Links
