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PDBsum entry 1n4y
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Blood clotting PDB id
1n4y

 

 

 

 

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Contents
Protein chain
68 a.a. *
* Residue conservation analysis
PDB id:
1n4y
Name: Blood clotting
Title: Refined structure of kistrin
Structure: Kistrin. Chain: a. Synonym: rhodostomin. Engineered: yes
Source: Calloselasma rhodostoma. Malayan pit viper. Organism_taxid: 8717. Gene: rhod. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 18 models
Authors: A.M.Krezel,J.Krane,M.S.Dennis,R.A.Lazarus,G.Wagner
Key ref: M.Adler et al. (1991). Solution structure of kistrin, a potent platelet aggregation inhibitor and GP IIb-IIIa antagonist. Science, 253, 445-448. PubMed id: 1862345 DOI: 10.1126/science.1862345
Date:
02-Nov-02     Release date:   28-Jan-03    
Supersedes: 1kst
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P30403  (VM2RH_CALRH) -  Zinc metalloproteinase/disintegrin from Calloselasma rhodostoma
Seq:
Struc: 		478 a.a.
68 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1126/science.1862345 Science 253:445-448 (1991)
PubMed id: 1862345  
 
 
Solution structure of kistrin, a potent platelet aggregation inhibitor and GP IIb-IIIa antagonist.
M.Adler, R.A.Lazarus, M.S.Dennis, G.Wagner.
 
  ABSTRACT  
 
The structure of kistrin, which is a member of a homologous family of glycoprotein IIb-IIIa (GP IIb-IIIa) antagonists and potent protein inhibitors of platelet aggregation, has been determined by two-dimensional nuclear magnetic resonance (NMR) spectroscopy. The 68-residue protein consists of a series of tightly packed loops held together by six disulfide bonds and has almost no regular secondary structure. Kistrin has an Arg-Gly-Asp (RGD) adhesion site recognition sequence important for binding to GP IIb-IIIa that is located at the apex of a long loop across the surface of the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16941670 K.L.White, M.Passipieri, T.D.Bunch, K.D.Campbell, and B.Pate (2007).
Effects of arginine-glycine-aspartic acid (RGD) containing snake venom peptides on parthenogenetic development and in vitro fertilization of bovine oocytes.
  Mol Reprod Dev, 74, 88-96.  
16279943 I.Simões, E.C.Mueller, A.Otto, D.Bur, A.Y.Cheung, C.Faro, and E.Pires (2005).
Molecular analysis of the interaction between cardosin A and phospholipase D(alpha). Identification of RGD/KGE sequences as binding motifs for C2 domains.
  FEBS J, 272, 5786-5798.  
16103990 X.Liu, X.Yan, W.Mo, H.Song, and L.Dai (2005).
1H NMR assignment and secondary structure of recombinant RGD-hirudin.
  Magn Reson Chem, 43, 956-961.  
15390258 J.H.Shiu, C.Y.Chen, L.S.Chang, Y.C.Chen, Y.C.Chen, Y.H.Lo, Y.C.Liu, and W.J.Chuang (2004).
Solution structure of gamma-bungarotoxin: the functional significance of amino acid residues flanking the RGD motif in integrin binding.
  Proteins, 57, 839-849.
PDB code: 1mr6
12815633 C.Rosselot, A.L.Kierszenbaum, E.Rivkin, and L.L.Tres (2003).
Chronological gene expression of ADAMs during testicular development: prespermatogonia (gonocytes) express fertilin beta (ADAM2).
  Dev Dyn, 227, 458-467.  
14661951 J.Shin, S.Y.Hong, K.Chung, I.Kang, Y.Jang, D.S.Kim, and W.Lee (2003).
Solution structure of a novel disintegrin, salmosin, from Agkistrondon halys venom.
  Biochemistry, 42, 14408-14415.
PDB codes: 1iq2 1l3x
12538900 M.P.Moreno-Murciano, D.Monleón, J.J.Calvete, B.Celda, and C.Marcinkiewicz (2003).
Amino acid sequence and homology modeling of obtustatin, a novel non-RGD-containing short disintegrin isolated from the venom of Vipera lebetina obtusa.
  Protein Sci, 12, 366-371.  
11468397 D.H.Souza, H.S.Selistre-de-Araujo, A.M.Moura-da-Silva, M.S.Della-Casa, G.Oliva, and R.C.Garratt (2001).
Crystallization and preliminary X-ray analysis of jararhagin, a metalloproteinase/disintegrin from Bothrops jararaca snake venom.
  Acta Crystallogr D Biol Crystallogr, 57, 1135-1137.  
11340665 R.T.Guo, L.J.Chou, Y.C.Chen, C.Y.Chen, K.Pari, C.J.Jen, S.J.Lo, S.L.Huang, C.Y.Lee, T.W.Chang, and W.J.Chaung (2001).
Expression in Pichia pastoris and characterization by circular dichroism and NMR of rhodostomin.
  Proteins, 43, 499-508.  
  10975565 A.M.Krezel, J.S.Ulmer, G.Wagner, and R.A.Lazarus (2000).
Recombinant decorsin: dynamics of the RGD recognition site.
  Protein Sci, 9, 1428-1438.  
11015207 B.Hu, D.Finsinger, K.Peter, Z.Guttenberg, M.Bärmann, H.Kessler, A.Escherich, L.Moroder, J.Böhm, W.Baumeister, S.F.Sui, and E.Sackmann (2000).
Intervesicle cross-linking with integrin alpha IIb beta 3 and cyclic-RGD-lipopeptide. A model of cell-adhesion processes.
  Biochemistry, 39, 12284-12294.  
  10933502 J.J.Calvete, M.P.Moreno-Murciano, L.Sanz, M.Jürgens, M.Schrader, M.Raida, D.C.Benjamin, and J.W.Fox (2000).
The disulfide bond pattern of catrocollastatin C, a disintegrin-like/cysteine-rich protein isolated from Crotalus atrox venom.
  Protein Sci, 9, 1365-1373.  
10862009 Y.Takahashi, N.Yamakawa, K.Matsumoto, Y.Toyoda, K.Furukawa, and E.Sato (2000).
Analysis of the role of egg integrins in sperm-egg binding and fusion.
  Mol Reprod Dev, 56, 412-423.  
9885189 A.Segura, M.Moreno, F.Madueño, A.Molina, and F.García-Olmedo (1999).
Snakin-1, a peptide from potato that is active against plant pathogens.
  Mol Plant Microbe Interact, 12, 16-23.  
  10400774 C.Y.Chiu, P.Mathias, G.R.Nemerow, and P.L.Stewart (1999).
Structure of adenovirus complexed with its internalization receptor, alphavbeta5 integrin.
  J Virol, 73, 6759-6768.  
10647183 E.Hendry, H.Hatanaka, E.Fry, M.Smyth, J.Tate, G.Stanway, J.Santti, M.Maaronen, T.Hyypiä, and D.Stuart (1999).
The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses.
  Structure, 7, 1527-1538.
PDB code: 1d4m
10563507 F.Vella, J.F.Hernandez, A.Molla, M.R.Block, and G.J.Arlaud (1999).
Grafting an RGD motif onto an epidermal growth factor-like module: chemical synthesis and functional characterization of the chimeric molecule.
  J Pept Res, 54, 415-426.  
9933744 H.J.Chang, S.Y.Sheu, and S.J.Lo (1999).
Expression of foreign antigens on the surface of Escherichia coli by fusion to the outer membrane protein traT.
  J Biomed Sci, 6, 64-70.  
10613901 M.Shiraga, A.Ritchie, S.Aidoudi, V.Baron, D.Wilcox, G.White, B.Ybarrondo, G.Murphy, A.Leavitt, and S.Shattil (1999).
Primary megakaryocytes reveal a role for transcription factor NF-E2 in integrin alpha IIb beta 3 signaling.
  J Cell Biol, 147, 1419-1430.  
9442878 D.J.Leahy (1997).
Implications of atomic-resolution structures for cell adhesion.
  Annu Rev Cell Dev Biol, 13, 363-393.  
  12386385 H.H.Chang, C.P.Chang, J.C.Chang, S.Z.Dung, and S.J.Lo (1997).
Application of Recombinant Rhodostomin in Studying Cell Adhesion.
  J Biomed Sci, 4, 235-243.  
9095678 J.A.Carver, G.Esposito, P.Viglino, F.Fogolari, G.Guichard, J.P.Briand, M.H.Van Regenmortel, F.Brown, and P.Mascagni (1997).
Structural comparison between retro-inverso and parent peptides: molecular basis for the biological activity of a retro-inverso analogue of the immunodominant fragment of VP1 coat protein from foot-and-mouth disease virus.
  Biopolymers, 41, 569-590.  
9070966 K.R.Chien, M.Shimizu, M.Hoshijima, S.Minamisawa, and A.A.Grace (1997).
Toward molecular strategies for heart disease--past, present, future.
  Jpn Circ J, 61, 91.  
9260929 M.R.Taylor, J.R.Couto, C.D.Scallan, R.L.Ceriani, and J.A.Peterson (1997).
Lactadherin (formerly BA46), a membrane-associated glycoprotein expressed in human milk and breast carcinomas, promotes Arg-Gly-Asp (RGD)-dependent cell adhesion.
  DNA Cell Biol, 16, 861-869.  
9135136 P.L.Stewart, C.Y.Chiu, S.Huang, T.Muir, Y.Zhao, B.Chait, P.Mathias, and G.R.Nemerow (1997).
Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes antibody neutralization.
  EMBO J, 16, 1189-1198.  
9268674 P.Lanza, B.Felding-Habermann, Z.M.Ruggeri, M.Zanetti, and R.Billetta (1997).
Selective interaction of a conformationally-constrained Arg-Gly-Asp (RGD) motif with the integrin receptor alphavbeta3 expressed on human tumor cells.
  Blood Cells Mol Dis, 23, 230-241.  
9105040 R.Yuan, P.Primakoff, and D.G.Myles (1997).
A role for the disintegrin domain of cyritestin, a sperm surface protein belonging to the ADAM family, in mouse sperm-egg plasma membrane adhesion and fusion.
  J Cell Biol, 137, 105-112.  
8939659 A.P.Huovila, E.A.Almeida, and J.M.White (1996).
ADAMs and cell fusion.
  Curr Opin Cell Biol, 8, 692-699.  
  8970152 B.Podbilewicz (1996).
ADM-1, a protein with metalloprotease- and disintegrin-like domains, is expressed in syncytial organs, sperm, and sheath cells of sensory organs in Caenorhabditis elegans.
  Mol Biol Cell, 7, 1877-1893.  
8548820 D.J.Leahy, I.Aukhil, and H.P.Erickson (1996).
2.0 A crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region.
  Cell, 84, 155-164.
PDB code: 1fnf
8639264 J.R.Couto, M.R.Taylor, S.G.Godwin, R.L.Ceriani, and J.A.Peterson (1996).
Cloning and sequence analysis of human breast epithelial antigen BA46 reveals an RGD cell adhesion sequence presented on an epidermal growth factor-like domain.
  DNA Cell Biol, 15, 281-286.  
8605193 K.H.Mayo, and F.Fan (1996).
Integrin receptor GPIIb/IIIa bound state conformation of the fibrinogen gamma-chain C-terminal peptide 400-411: NMR and transfer NOE studies.
  Biochemistry, 35, 4434-4444.  
8919879 P.A.McLenachan, P.J.Lockhart, H.R.Faber, and B.C.Mansfield (1996).
Evolutionary analysis of the multigene pregnancy-specific beta 1-glycoprotein family: separation of historical and nonhistorical signals.
  J Mol Evol, 42, 273-280.  
8846226 B.Zhao, L.R.Helms, R.L.DesJarlais, S.S.Abdel-Meguid, and R.Wetzel (1995).
A paradigm for drug discovery using a conformation from the crystal structure of a presentation scaffold.
  Nat Struct Biol, 2, 1131-1137.  
7600577 E.A.Almeida, A.P.Huovila, A.E.Sutherland, L.E.Stephens, P.G.Calarco, L.M.Shaw, A.M.Mercurio, A.Sonnenberg, P.Primakoff, D.G.Myles, and J.M.White (1995).
Mouse egg integrin alpha 6 beta 1 functions as a sperm receptor.
  Cell, 81, 1095-1104.  
  7773176 M.P.Egloff, L.Sarda, R.Verger, C.Cambillau, and H.van Tilbeurgh (1995).
Crystallographic study of the structure of colipase and of the interaction with pancreatic lipase.
  Protein Sci, 4, 44-57.  
7925406 C.Reisdorf, D.Abergel, F.Bontems, J.Y.Lallemand, J.P.Decottignies, and G.Spik (1994).
Proton resonance assignments and secondary structure of bovine angiogenin.
  Eur J Biochem, 224, 811-822.  
8183890 D.G.Myles, L.H.Kimmel, C.P.Blobel, J.M.White, and P.Primakoff (1994).
Identification of a binding site in the disintegrin domain of fertilin required for sperm-egg fusion.
  Proc Natl Acad Sci U S A, 91, 4195-4198.  
7738606 G.Müller, M.Gurrath, and H.Kessler (1994).
Pharmacophore refinement of gpIIb/IIIa antagonists based on comparative studies of antiadhesive cyclic and acyclic RGD peptides.
  J Comput Aided Mol Des, 8, 709-730.  
8081748 I.D.Campbell, and C.Spitzfaden (1994).
Building proteins with fibronectin type III modules.
  Structure, 2, 333-337.  
8191932 K.L.King, J.J.D'Anza, S.Bodary, R.Pitti, M.Siegel, R.A.Lazarus, M.S.Dennis, R.G.Hammonds, and S.C.Kukreja (1994).
Effects of kistrin on bone resorption in vitro and serum calcium in vivo.
  J Bone Miner Res, 9, 381-387.  
7634091 M.J.Sutcliffe, M.Jaseja, E.I.Hyde, X.Lu, and J.A.Williams (1994).
Three-dimensional structure of the RGD-containing neurotoxin homologue dendroaspin.
  Nat Struct Biol, 1, 802-807.
PDB code: 1drs
7813476 M.Jaseja, X.Lu, J.A.Williams, M.J.Sutcliffe, V.V.Kakkar, R.A.Parslow, and E.I.Hyde (1994).
1H-NMR assignments and secondary structure of dendroaspin, an RGD-containing glycoprotein IIb-IIIa (alpha IIb-beta 3) antagonist with a neurotoxin fold.
  Eur J Biochem, 226, 861-868.  
8127909 P.W.Mason, E.Rieder, and B.Baxt (1994).
RGD sequence of foot-and-mouth disease virus is essential for infecting cells via the natural receptor but can be bypassed by an antibody-dependent enhancement pathway.
  Proc Natl Acad Sci U S A, 91, 1932-1936.  
8081743 S.Lea, J.Hernández, W.Blakemore, E.Brocchi, S.Curry, E.Domingo, E.Fry, R.Abu-Ghazaleh, A.King, and J.Newman (1994).
The structure and antigenicity of a type C foot-and-mouth disease virus.
  Structure, 2, 123-139.
PDB code: 1fmd
7694276 C.F.Barbas, L.R.Languino, and J.W.Smith (1993).
High-affinity self-reactive human antibodies by design and selection: targeting the integrin ligand binding site.
  Proc Natl Acad Sci U S A, 90, 10003-10007.  
8117416 D.S.Tuckwell, and M.J.Humphries (1993).
Molecular and cellular biology of integrins.
  Crit Rev Oncol Hematol, 15, 149-171.  
8456095 G.Müller, M.Gurrath, M.Kurz, and H.Kessler (1993).
Beta VI turns in peptides and proteins: a model peptide mimicry.
  Proteins, 15, 235-251.  
8281937 M.Jaseja, K.J.Smith, X.Lu, J.A.Williams, H.Trayer, I.P.Trayer, and E.I.Hyde (1993).
1H-NMR studies and secondary structure of the RGD-containing snake toxin, albolabrin.
  Eur J Biochem, 218, 853-860.  
8456099 M.S.Dennis, P.Carter, and R.A.Lazarus (1993).
Binding interactions of kistrin with platelet glycoprotein IIb-IIIa: analysis by site-directed mutagenesis.
  Proteins, 15, 312-321.  
  8223447 M.Zanetti, G.Filaci, R.H.Lee, P.del Guercio, F.Rossi, R.Bacchetta, F.Stevenson, V.Barnaba, and R.Billetta (1993).
Expression of conformationally constrained adhesion peptide in an antibody CDR loop and inhibition of natural killer cell cytotoxic activity by an antibody antigenized with the RGD motif.
  EMBO J, 12, 4375-4384.  
7763974 R.A.Lazarus, and R.S.McDowell (1993).
Structural and functional aspects of RGD-containing protein antagonists of glycoprotein IIb-IIIa.
  Curr Opin Biotechnol, 4, 438-445.  
8248170 T.G.Wolfsberg, J.F.Bazan, C.P.Blobel, D.G.Myles, P.Primakoff, and J.M.White (1993).
The precursor region of a protein active in sperm-egg fusion contains a metalloprotease and a disintegrin domain: structural, functional, and evolutionary implications.
  Proc Natl Acad Sci U S A, 90, 10783-10787.  
  8251946 W.R.Gray (1993).
Echistatin disulfide bridges: selective reduction and linkage assignment.
  Protein Sci, 2, 1749-1755.  
1423622 A.L.Main, T.S.Harvey, M.Baron, J.Boyd, and I.D.Campbell (1992).
The three-dimensional structure of the tenth type III module of fibronectin: an insight into RGD-mediated interactions.
  Cell, 71, 671-678.
PDB codes: 1ttf 1ttg
1419054 C.P.Blobel, and J.M.White (1992).
Structure, function and evolutionary relationship of proteins containing a disintegrin domain.
  Curr Opin Cell Biol, 4, 760-765.  
1320418 G.Wagner, V.Thanabal, B.J.Stockman, J.W.Peng, N.R.Nirmala, S.G.Hyberts, M.S.Goldberg, D.J.Detlefsen, R.T.Clubb, and M.Adler (1992).
NMR studies of structure and dynamics of isotope enriched proteins.
  Biopolymers, 32, 381-390.  
1483474 M.Gurrath, G.Müller, H.Kessler, M.Aumailley, and R.Timpl (1992).
Conformation/activity studies of rationally designed potent anti-adhesive RGD peptides.
  Eur J Biochem, 210, 911-921.  
1419055 M.H.Ginsberg, X.Du, and E.F.Plow (1992).
Inside-out integrin signalling.
  Curr Opin Cell Biol, 4, 766-771.  
1368432 W.J.Chazin (1992).
NMR structures and methodology.
  Curr Opin Biotechnol, 3, 326-332.  
1765068 P.Mazur, W.J.Henzel, J.L.Seymour, and R.A.Lazarus (1991).
Ornatins: potent glycoprotein IIb-IIIa antagonists and platelet aggregation inhibitors from the leech Placobdella ornata.
  Eur J Biochem, 202, 1073-1082.  
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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