 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Blood clotting
|
PDB id
|
|
|
|
2h43
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
70 a.a.
|
|
|
|
|
|
|
|
|
|
|
302 a.a.
|
|
|
|
|
|
|
|
|
|
|
290 a.a.
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Blood clotting
|
|
|
Title:
|
|
Crystal structure of human fragment d complexed with ala-his amide
|
|
Structure:
|
|
Fibrinogen alpha chain. Chain: a, d. Fibrinogen beta chain. Chain: b, e. Fibrinogen gamma chain. Chain: c, f. Gly-his-arg-pro-amide peptide ligand. Chain: i, j. Engineered: yes
|
|
Source:
|
|
Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Other_details: the peptide was chemically synthesized.
|
|
Biol. unit:
|
|
Tetramer (from
)
|
|
Resolution:
|
|
|
2.70Å
|
R-factor:
|
0.251
|
R-free:
|
0.307
|
|
|
Authors:
|
|
R.F.Doolittle,L.Pandi
|
Key ref:
|
|
R.F.Doolittle
et al.
(2006).
Differences in binding specificity for the homologous gamma- and beta-chain "holes" on fibrinogen: exclusive binding of Ala-His-Arg-Pro-amide by the beta-chain hole.
Biochemistry,
45,
13962-13969.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
23-May-06
|
Release date:
|
05-Dec-06
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
|
|
|
|
P02671
(FIBA_HUMAN) -
Fibrinogen alpha chain
|
|
|
|
Seq:
Struc:
|
|
|
|
866 a.a.
70 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Gene Ontology (GO) functional annotation
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Cellular component
|
extracellular space
|
2 terms
|
|
|
Biological process
|
signal transduction
|
3 terms
|
|
|
Biochemical function
|
receptor binding
|
2 terms
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
45:13962-13969
(2006)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Differences in binding specificity for the homologous gamma- and beta-chain "holes" on fibrinogen: exclusive binding of Ala-His-Arg-Pro-amide by the beta-chain hole.
|
|
R.F.Doolittle,
A.Chen,
L.Pandi.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The beta-chain amino-terminal sequences of all known mammalian fibrins begin
with the sequence Gly-His-Arg-Pro- (GHRP-), but the homologous sequence in
chicken fibrin begins with the sequence Ala-His-Arg-Pro- (AHRP-). Nonetheless,
chicken fibrinogen binds the synthetic peptide GHRPam, and a previously reported
crystal structure has revealed that the binding is in exact conformance with
that observed for the human GHRPam-fragment D complex. We now report that human
fibrinogen, which is known not to bind APRP, binds the synthetic peptide AHRPam.
Moreover, a crystal structure of AHRPam complexed with fragment D from human
fibrinogen shows that AHRPam binds exclusively to the beta-chain hole and,
unlike GHRPam, not at all to the homologous gamma-chain hole. The difference can
be attributed to the methyl group of the alanine residue clashing with a
critical carboxyl group in the gammaC hole but being accommodated in the roomier
betaC hole where the equivalent carboxyl is situated more flexibly.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
S.E.Stabenfeldt,
J.J.Gossett,
and
T.H.Barker
(2010).
Building better fibrin knob mimics: an investigation of synthetic fibrin knob peptide structures in solution and their dynamic binding with fibrinogen/fibrin holes.
|
| |
Blood, 116,
1352-1359.
|
|
|
|
|
|
|
I.Parastatidis,
L.Thomson,
A.Burke,
I.Chernysh,
C.Nagaswami,
J.Visser,
S.Stamer,
D.C.Liebler,
G.Koliakos,
H.F.Heijnen,
G.A.Fitzgerald,
J.W.Weisel,
and
H.Ischiropoulos
(2008).
Fibrinogen beta-chain tyrosine nitration is a prothrombotic risk factor.
|
| |
J Biol Chem, 283,
33846-33853.
|
|
|
|
|
|
|
C.B.Geer,
A.Tripathy,
M.H.Schoenfisch,
S.T.Lord,
and
O.V.Gorkun
(2007).
Role of 'B-b' knob-hole interactions in fibrin binding to adsorbed fibrinogen.
|
| |
J Thromb Haemost, 5,
2344-2351.
|
|
|
|
|
|
|
M.Guthold,
W.Liu,
E.A.Sparks,
L.M.Jawerth,
L.Peng,
M.Falvo,
R.Superfine,
R.R.Hantgan,
and
S.T.Lord
(2007).
A comparison of the mechanical and structural properties of fibrin fibers with other protein fibers.
|
| |
Cell Biochem Biophys, 49,
165-181.
|
|
|
|
|
|
|
S.T.Lord
(2007).
Fibrinogen and fibrin: scaffold proteins in hemostasis.
|
| |
Curr Opin Hematol, 14,
236-241.
|
|
|
|
|
|
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.
|
| | |
Links
