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PDBsum entry 3ghg
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Blood clotting
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PDB id
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3ghg
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Contents |
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174 a.a.
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401 a.a.
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381 a.a.
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186 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Blood clotting
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Title:
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Crystal structure of human fibrinogen
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Structure:
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Fibrinogen alpha chain. Chain: a, d, g, j. Fragment: mature chain. Fibrinogen beta chain. Chain: b, e, h, k. Fragment: mature chain. Fibrinogen gamma chain. Chain: c, f, i, l. Fragment: mature chain.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood plasma. Synthetic: yes. Synthetic: yes
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Resolution:
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2.90Å
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R-factor:
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0.255
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R-free:
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0.309
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Authors:
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R.F.Doolittle,J.M.Kollman,M.R.Sawaya,L.Pandi,M.Riley
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Key ref:
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J.M.Kollman
et al.
(2009).
Crystal structure of human fibrinogen.
Biochemistry,
48,
3877-3886.
PubMed id:
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Date:
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03-Mar-09
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Release date:
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19-May-09
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PROCHECK
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Headers
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References
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P02671
(FIBA_HUMAN) -
Fibrinogen alpha chain from Homo sapiens
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Seq:
Struc:
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866 a.a.
174 a.a.
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P02675
(FIBB_HUMAN) -
Fibrinogen beta chain from Homo sapiens
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Seq:
Struc:
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491 a.a.
401 a.a.
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Biochemistry
48:3877-3886
(2009)
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PubMed id:
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Crystal structure of human fibrinogen.
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J.M.Kollman,
L.Pandi,
M.R.Sawaya,
M.Riley,
R.F.Doolittle.
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ABSTRACT
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A crystal structure of human fibrinogen has been determined at approximately 3.3
A resolution. The protein was purified from human blood plasma, first by a cold
ethanol precipitation procedure and then by stepwise chromatography on
DEAE-cellulose. A product was obtained that was homogeneous on
SDS-polyacrylamide gels. Nonetheless, when individual crystals used for X-ray
diffraction were examined by SDS gel electrophoresis after data collection, two
species of alpha chain were present, indicating that some proteolysis had
occurred during the course of operations. Amino-terminal sequencing on
post-X-ray crystals showed mostly intact native alpha- and gamma-chain sequences
(the native beta chain is blocked). The overall structure differs from that of a
native fibrinogen from chicken blood and those reported for a partially
proteolyzed bovine fibrinogen in the nature of twist in the coiled-coil regions,
likely due to weak forces imparted by unique crystal packing. As such, the
structure adds to the inventory of possible conformations that may occur in
solution. Other features include a novel interface with an antiparallel
arrangement of beta chains and a unique tangential association of coiled coils
from neighboring molecules. The carbohydrate groups attached to beta chains are
unusually prominent, the full sweep of 11 sugar residues being positioned. As
was the case for native chicken fibrinogen, no resolvable electron density could
be associated with alphaC domains.
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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.F.Schilke,
and
J.McGuire
(2011).
Detection of nisin and fibrinogen adsorption on poly(ethylene oxide) coated polyurethane surfaces by time-of-flight secondary ion mass spectrometry (TOF-SIMS).
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J Colloid Interface Sci,
358,
14-24.
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P.Macheboeuf,
C.Buffalo,
C.Y.Fu,
A.S.Zinkernagel,
J.N.Cole,
J.E.Johnson,
V.Nizet,
and
P.Ghosh
(2011).
Streptococcal M1 protein constructs a pathological host fibrinogen network.
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Nature,
472,
64-68.
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PDB codes:
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T.Riedel,
J.Suttnar,
E.Brynda,
M.Houska,
L.Medved,
and
J.E.Dyr
(2011).
Fibrinopeptides A and B release in the process of surface fibrin formation.
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Blood,
117,
1700-1706.
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V.M.Gun'ko,
L.I.Mikhalovska,
P.E.Tomlins,
and
S.V.Mikhalovsky
(2011).
Competitive adsorption of macromolecules and real-time dynamics of Vroman-like effects.
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Phys Chem Chem Phys,
13,
4476-4485.
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M.Corno,
A.Rimola,
V.Bolis,
and
P.Ugliengo
(2010).
Hydroxyapatite as a key biomaterial: quantum-mechanical simulation of its surfaces in interaction with biomolecules.
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Phys Chem Chem Phys,
12,
6309-6329.
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W.Liu,
C.R.Carlisle,
E.A.Sparks,
and
M.Guthold
(2010).
The mechanical properties of single fibrin fibers.
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J Thromb Haemost,
8,
1030-1036.
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G.Tsurupa,
R.R.Hantgan,
R.A.Burton,
I.Pechik,
N.Tjandra,
and
L.Medved
(2009).
Structure, stability, and interaction of the fibrin(ogen) alphaC-domains.
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Biochemistry,
48,
12191-12201.
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J.W.Weisel
(2009).
Why dysfibrinogenaemias still matter.
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Thromb Haemost,
102,
426-427.
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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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