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PDBsum entry 2gdt
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Viral protein, hydrolase
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PDB id
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2gdt
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PDB id:
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| Name: |
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Viral protein, hydrolase
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Title:
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Nmr structure of the nonstructural protein 1 (nsp1) from the sars coronavirus
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Structure:
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Leader protein. P65 homolog. Nsp1 (ec 3.4.22.-). Chain: a. Fragment: nsp1-6. Engineered: yes. Mutation: yes
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Source:
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Sars coronavirus. Organism_taxid: 227859. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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NMR struc:
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20 models
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Authors:
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M.S.Almeida,T.Herrmann,M.Geralt,M.A.Johnson,K.Saikatendu,J.Joseph, R.C.Subramanian,B.W.Neuman,M.J.Buchmeier,R.C.Stevens,P.Kuhn, I.A.Wilson,K.Wuthrich,Joint Center For Structural Genomics (Jcsg)
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Key ref:
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M.S.Almeida
et al.
(2007).
Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.
J Virol,
81,
3151-3161.
PubMed id:
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Date:
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17-Mar-06
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Release date:
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06-Feb-07
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PROCHECK
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Headers
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References
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P0C6X7
(R1AB_CVHSA) -
Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus
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Seq:
Struc:
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7073 a.a.
116 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class 2:
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E.C.2.1.1.-
- ?????
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Enzyme class 3:
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E.C.2.1.1.56
- mRNA (guanine-N(7))-methyltransferase.
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Reaction:
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a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
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5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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S-adenosyl-L- methionine
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=
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5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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S-adenosyl-L-homocysteine
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Enzyme class 4:
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E.C.2.1.1.57
- methyltransferase cap1.
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Reaction:
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a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H+
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5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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S-adenosyl-L-methionine
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=
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5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA
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+
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S-adenosyl-L-homocysteine
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+
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H(+)
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Enzyme class 5:
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E.C.2.7.7.48
- RNA-directed Rna polymerase.
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Reaction:
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RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
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RNA(n)
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+
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ribonucleoside 5'-triphosphate
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=
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RNA(n+1)
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+
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diphosphate
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Enzyme class 6:
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E.C.2.7.7.50
- mRNA guanylyltransferase.
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Reaction:
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a 5'-end diphospho-ribonucleoside in mRNA + GTP + H+ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate
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5'-end diphospho-ribonucleoside in mRNA
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+
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GTP
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+
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H(+)
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=
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5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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diphosphate
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Enzyme class 7:
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E.C.3.1.13.-
- ?????
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Enzyme class 8:
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E.C.3.4.19.12
- ubiquitinyl hydrolase 1.
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Reaction:
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Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
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Enzyme class 9:
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E.C.3.4.22.-
- ?????
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Enzyme class 10:
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E.C.3.4.22.69
- Sars coronavirus main proteinase.
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Enzyme class 11:
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E.C.3.6.4.12
- Dna helicase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
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+
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H2O
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=
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ADP
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+
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phosphate
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+
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H(+)
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Enzyme class 12:
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E.C.3.6.4.13
- Rna helicase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
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+
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H2O
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=
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ADP
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+
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phosphate
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+
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H(+)
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Enzyme class 13:
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E.C.4.6.1.-
- ?????
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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J Virol
81:3151-3161
(2007)
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PubMed id:
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Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.
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M.S.Almeida,
M.A.Johnson,
T.Herrmann,
M.Geralt,
K.Wüthrich.
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ABSTRACT
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The nonstructural protein 1 (nsp1) of the severe acute respiratory syndrome
coronavirus has 179 residues and is the N-terminal cleavage product of the viral
replicase polyprotein that mediates RNA replication and processing. The specific
function of nsp1 is not known. Here we report the nuclear magnetic resonance
structure of the nsp1 segment from residue 13 to 128, which represents a novel
alpha/beta-fold formed by a mixed parallel/antiparallel six-stranded
beta-barrel, an alpha-helix covering one opening of the barrel, and a
3(10)-helix alongside the barrel. We further characterized the full-length
179-residue protein and show that the polypeptide segments of residues 1 to 12
and 129 to 179 are flexibly disordered. The structure is analyzed in a search
for possible correlations with the recently reported activity of nsp1 in the
degradation of mRNA.
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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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K.M.Gustin,
B.J.Guan,
A.Dziduszko,
and
D.A.Brian
(2009).
Bovine coronavirus nonstructural protein 1 (p28) is an RNA binding protein that binds terminal genomic cis-replication elements.
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J Virol,
83,
6087-6097.
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P.Serrano,
M.A.Johnson,
A.Chatterjee,
B.W.Neuman,
J.S.Joseph,
M.J.Buchmeier,
P.Kuhn,
and
K.Wüthrich
(2009).
Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3.
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J Virol,
83,
12998-13008.
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PDB code:
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S.Perlman,
and
J.Netland
(2009).
Coronaviruses post-SARS: update on replication and pathogenesis.
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Nat Rev Microbiol,
7,
439-450.
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B.Canard,
J.S.Joseph,
and
P.Kuhn
(2008).
International research networks in viral structural proteomics: again, lessons from SARS.
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Antiviral Res,
78,
47-50.
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C.Zhang,
O.Crasta,
S.Cammer,
R.Will,
R.Kenyon,
D.Sullivan,
Q.Yu,
W.Sun,
R.Jha,
D.Liu,
T.Xue,
Y.Zhang,
M.Moore,
P.McGarvey,
H.Huang,
Y.Chen,
J.Zhang,
R.Mazumder,
C.Wu,
and
B.Sobral
(2008).
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.
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Nucleic Acids Res,
36,
D884-D891.
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H.P.Narra,
M.H.Cordes,
and
H.Ochman
(2008).
Structural features and the persistence of acquired proteins.
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Proteomics,
8,
4772-4781.
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K.Narayanan,
C.Huang,
K.Lokugamage,
W.Kamitani,
T.Ikegami,
C.T.Tseng,
and
S.Makino
(2008).
Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells.
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J Virol,
82,
4471-4479.
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M.Bartlam,
X.Xue,
and
Z.Rao
(2008).
The search for a structural basis for therapeutic intervention against the SARS coronavirus.
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Acta Crystallogr A,
64,
204-213.
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Y.Shen,
O.Lange,
F.Delaglio,
P.Rossi,
J.M.Aramini,
G.Liu,
A.Eletsky,
Y.Wu,
K.K.Singarapu,
A.Lemak,
A.Ignatchenko,
C.H.Arrowsmith,
T.Szyperski,
G.T.Montelione,
D.Baker,
and
A.Bax
(2008).
Consistent blind protein structure generation from NMR chemical shift data.
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Proc Natl Acad Sci U S A,
105,
4685-4690.
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M.Bartlam,
Y.Xu,
and
Z.Rao
(2007).
Structural proteomics of the SARS coronavirus: a model response to emerging infectious diseases.
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J Struct Funct Genomics,
8,
85-97.
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R.Züst,
L.Cervantes-Barragán,
T.Kuri,
G.Blakqori,
F.Weber,
B.Ludewig,
and
V.Thiel
(2007).
Coronavirus non-structural protein 1 is a major pathogenicity factor: implications for the rational design of coronavirus vaccines.
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PLoS Pathog,
3,
e109.
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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
