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Coagulation factor binding PDB id
1ixx
Jmol
Contents
Protein chains
129 a.a. *
123 a.a. *
Metals
_CA ×6
Waters ×146
* Residue conservation analysis
PDB id:
1ixx
Name: Coagulation factor binding
Title: Crystal structure of coagulation factors ix/x-binding protei bp) from venom of habu snake with a heterodimer of c-type l domains
Structure: Coagulation factors ix/x-binding protein. Chain: a, c, e. Fragment: c-type lectin domain. Synonym: ix/x-bp. Coagulation factors ix/x-binding protein. Chain: b, d, f. Fragment: c-type lectin domain. Synonym: ix/x-bp
Source: Trimeresurus flavoviridis. Organism_taxid: 88087. Secretion: venom. Secretion: venom
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.178     R-free:   0.221
Authors: H.Mizuno,Z.Fujimoto,M.Koizumi,H.Kano
Key ref: H.Mizuno et al. (1997). Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains. Nat Struct Biol, 4, 438-441. PubMed id: 9187649 DOI: 10.1038/nsb0697-438
Date:
01-May-97     Release date:   06-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23806  (IXXA_TRIFL) -  Coagulation factor IX/factor X-binding protein subunit A
Seq:
Struc: 		152 a.a.
129 a.a.
Protein chains
Pfam   ArchSchema ?
P23807  (IXXB_TRIFL) -  Coagulation factor IX/factor X-binding protein subunit B
Seq:
Struc: 		146 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     blood coagulation   1 term 
  Biochemical function     binding     3 terms  

 

 
DOI no: 10.1038/nsb0697-438 Nat Struct Biol 4:438-441 (1997)
PubMed id: 9187649  
 
 
Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains.
H.Mizuno, Z.Fujimoto, M.Koizumi, H.Kano, H.Atoda, T.Morita.
 
  ABSTRACT  
 
Coagulation factors IX/X-binding protein is an intertwined dimer with a central loop projecting into the adjoining subunit. Excluding this loop, each subunit has a fold similar to rat mannose-binding protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21197556 D.Shen, X.Xu, H.Wu, L.Peng, Y.Zhang, J.Song, and Q.Su (2011).
Metal ion binding to anticoagulation factor II from the venom of Agkistrodon acutus: stabilization of the structure and regulation of the binding affinity to activated coagulation factor X.
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20091872 R.P.Nagarkar, R.A.Hule, D.J.Pochan, and J.P.Schneider (2010).
Domain swapping in materials design.
  Biopolymers, 94, 141-155.  
18977769 M.Ishikawa, M.Kumashiro, Y.Yamazaki, H.Atoda, and T.Morita (2009).
Anticoagulant Mechanism of Factor IX/factor X-binding Protein Isolated from the Venom of Trimeresurus flavoviridis.
  J Biochem, 145, 123-128.  
19495561 R.Doley, and R.M.Kini (2009).
Protein complexes in snake venom.
  Cell Mol Life Sci, 66, 2851-2871.  
19184130 X.Xu, L.Zhang, D.Shen, H.Wu, L.Peng, and J.Li (2009).
Effect of metal ion substitutions in anticoagulation factor I from the venom of Agkistrodon acutus on the binding of activated coagulation factor X and on structural stability.
  J Biol Inorg Chem, 14, 559-571.  
18583525 A.A.Watson, J.A.Eble, and C.A.O'Callaghan (2008).
Crystal structure of rhodocytin, a ligand for the platelet-activating receptor CLEC-2.
  Protein Sci, 17, 1611-1616.
PDB code: 2vrp
18597489 E.Hooley, E.Papagrigoriou, A.Navdaev, A.V.Pandey, J.M.Clemetson, K.J.Clemetson, and J.Emsley (2008).
The crystal structure of the platelet activator aggretin reveals a novel (alphabeta)2 dimeric structure.
  Biochemistry, 47, 7831-7837.
PDB code: 3bx4
18616470 H.S.Chen, J.M.Chen, C.W.Lin, K.H.Khoo, and I.H.Tsai (2008).
New insights into the functions and N-glycan structures of factor X activator from Russell's viper venom.
  FEBS J, 275, 3944-3958.  
17279335 X.Xu, J.Chen, L.Zhang, S.Wang, D.Shen, and Q.Liu (2007).
Calcium ion-induced stabilization and refolding of agkisacutacin from Agkistrodon acutus venom studied by fluorescent spectroscopy.
  J Fluoresc, 17, 215-221.  
16627619 T.U.Schwartz, D.Schmidt, S.G.Brohawn, and G.Blobel (2006).
Homodimerization of the G protein SRbeta in the nucleotide-free state involves proline cis/trans isomerization in the switch II region.
  Proc Natl Acad Sci U S A, 103, 6823-6828.
PDB code: 2ged
16206329 A.Bazaa, N.Marrakchi, M.El Ayeb, L.Sanz, and J.J.Calvete (2005).
Snake venomics: comparative analysis of the venom proteomes of the Tunisian snakes Cerastes cerastes, Cerastes vipera and Macrovipera lebetina.
  Proteomics, 5, 4223-4235.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
  16508118 N.Suzuki, Y.Shikamoto, Z.Fujimoto, T.Morita, and H.Mizuno (2005).
Crystallization and preliminary X-ray analysis of coagulation factor IX-binding protein from habu snake venom at pH 6.5 and 4.6.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 147-149.  
15576563 P.Paaventhan, C.Kong, J.S.Joseph, M.C.Chung, and P.R.Kolatkar (2005).
Structure of rhodocetin reveals noncovalently bound heterodimer interface.
  Protein Sci, 14, 169-175.
PDB code: 1sb2
15863880 S.Sugawara, M.Hosono, Y.Ogawa, M.Takayanagi, and K.Nitta (2005).
Molecular and sugar-binding heterogeneity of C-type lectins from Osmerus (Spirinchus) lanceolatus eggs.
  Biol Pharm Bull, 28, 791-796.  
15502319 G.Xu, M.Teng, L.Niu, P.Liu, Y.Dong, Q.Liu, Q.Huang, and Q.Hao (2004).
Purification, characterization, crystallization and preliminary X-ray crystallographic analysis of two novel C-type lectin-like proteins: Aall-A and Aall-B from Deinagkistrodon acutus venom.
  Acta Crystallogr D Biol Crystallogr, 60, 2035-2037.  
15319425 H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, and T.Hatakeyama (2004).
Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type Lectin, CEL-I, revealed by X-ray crystallographic analysis.
  J Biol Chem, 279, 45219-45225.
PDB codes: 1wmy 1wmz
15140887 R.Guan, E.L.Malchiodi, Q.Wang, P.Schuck, and R.A.Mariuzza (2004).
Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha.
  J Biol Chem, 279, 31873-31882.
PDB codes: 1sk3 1sk4
12866057 A.N.Zelensky, and J.E.Gready (2003).
Comparative analysis of structural properties of the C-type-lectin-like domain (CTLD).
  Proteins, 52, 466-477.  
14580195 K.Horii, D.Okuda, T.Morita, and H.Mizuno (2003).
Structural characterization of EMS16, an antagonist of collagen receptor (GPIa/IIa) from the venom of Echis multisquamatus.
  Biochemistry, 42, 12497-12502.
PDB code: 1ukm
12851390 N.Maita, K.Nishio, E.Nishimoto, T.Matsui, Y.Shikamoto, T.Morita, J.E.Sadler, and H.Mizuno (2003).
Crystal structure of von Willebrand factor A1 domain complexed with snake venom, bitiscetin: insight into glycoprotein Ibalpha binding mechanism induced by snake venom proteins.
  J Biol Chem, 278, 37777-37781.
PDB code: 1uex
12945048 S.Ebner, N.Sharon, and N.Ben-Tal (2003).
Evolutionary analysis reveals collective properties and specificity in the C-type lectin and lectin-like domain superfamily.
  Proteins, 53, 44-55.  
11856355 J.C.Achenbach, and K.V.Ewart (2002).
Structural and functional characterization of a C-type lectin-like antifreeze protein from rainbow smelt (Osmerus mordax).
  Eur J Biochem, 269, 1219-1226.  
11861620 K.Natarajan, N.Dimasi, J.Wang, R.A.Mariuzza, and D.H.Margulies (2002).
Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination.
  Annu Rev Immunol, 20, 853-885.  
11866098 T.Hatakeyama, N.Matsuo, K.Shiba, S.Nishinohara, N.Yamasaki, H.Sugawara, and H.Aoyagi (2002).
Amino acid sequence and carbohydrate-binding analysis of the N-acetyl-D-galactosamine-specific C-type lectin, CEL-I, from the Holothuroidea, Cucumaria echinata.
  Biosci Biotechnol Biochem, 66, 157-163.  
11910037 X.Xu, Q.Liu, H.Yu, and Y.Xie (2002).
Ca(II)- and Tb(III)-induced stabilization and refolding of anticoagulation factor I from the venom of Agkistrodon acutus.
  Protein Sci, 11, 944-956.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
12047379 Y.Yamazaki, H.Koike, Y.Sugiyama, K.Motoyoshi, T.Wada, S.Hishinuma, M.Mita, and T.Morita (2002).
Cloning and characterization of novel snake venom proteins that block smooth muscle contraction.
  Eur J Biochem, 269, 2708-2715.  
11785767 H.Kogelberg, and T.Feizi (2001).
New structural insights into lectin-type proteins of the immune system.
  Curr Opin Struct Biol, 11, 635-643.  
11404471 H.Mizuno, Z.Fujimoto, H.Atoda, and T.Morita (2001).
Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X.
  Proc Natl Acad Sci U S A, 98, 7230-7234.
PDB code: 1iod
11148028 U.Sen, S.Vasudevan, G.Subbarao, R.A.McClintock, R.Celikel, Z.M.Ruggeri, and K.I.Varughese (2001).
Crystal structure of the von Willebrand factor modulator botrocetin.
  Biochemistry, 40, 345-352.
PDB code: 1fvu
10813833 H.Zhang, K.Huang, Z.Li, L.Banerjei, K.E.Fisher, N.V.Grishin, E.Eisenstein, and O.Herzberg (2000).
Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.
  Proteins, 40, 86-97.
PDB codes: 1dbu 1dbx
10684640 K.Fukuda, H.Mizuno, H.Atoda, and T.Morita (2000).
Crystal structure of flavocetin-A, a platelet glycoprotein Ib-binding protein, reveals a novel cyclic tetramer of C-type lectin-like heterodimers.
  Biochemistry, 39, 1915-1923.
PDB code: 1c3a
  11045608 K.Håkansson, and K.B.Reid (2000).
Collectin structure: a review.
  Protein Sci, 9, 1607-1617.  
10023772 J.C.Boyington, A.N.Riaz, A.Patamawenu, J.E.Coligan, A.G.Brooks, and P.D.Sun (1999).
Structure of CD94 reveals a novel C-type lectin fold: implications for the NK cell-associated CD94/NKG2 receptors.
  Immunity, 10, 75-82.
PDB code: 1b6e
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
9860851 H.Atoda, M.Ishikawa, H.Mizuno, and T.Morita (1998).
Coagulation factor X-binding protein from Deinagkistrodon acutus venom is a Gla domain-binding protein.
  Biochemistry, 37, 17361-17370.  
9786936 J.H.Graversen, R.H.Lorentsen, C.Jacobsen, S.K.Moestrup, B.W.Sigurskjold, H.C.Thogersen, and M.Etzerodt (1998).
The plasminogen binding site of the C-type lectin tetranectin is located in the carbohydrate recognition domain, and binding is sensitive to both calcium and lysine.
  J Biol Chem, 273, 29241-29246.  
9724722 Y.H.Ding, K.Javaherian, K.M.Lo, R.Chopra, T.Boehm, J.Lanciotti, B.A.Harris, Y.Li, R.Shapiro, E.Hohenester, R.Timpl, J.Folkman, and D.C.Wiley (1998).
Zinc-dependent dimers observed in crystals of human endostatin.
  Proc Natl Acad Sci U S A, 95, 10443-10448.
PDB code: 1bnl
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.