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PDBsum entry 1kjd

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protein metals links
Cell adhesion protein PDB id
1kjd
Jmol
Contents
Protein chain
120 a.a.
Metals
_CA
Theoretical model
PDB id:
1kjd
Name: Cell adhesion protein
Title: Theoretical model of p-selectin, c-type lectin domain, residues 1-120, cell adhesion molecule
Structure: P-selectin. Chain: null. Fragment: c-type lectin domain, residues 1 - 120
Source: Homo sapiens. Human
Authors: J.Bajorath,R.Stenkamp,A.Aruffo
Key ref:
J.Bajorath et al. (1993). Knowledge-based model building of proteins: concepts and examples. Protein Sci, 2, 1798-1810. PubMed id: 7505680 DOI: 10.1002/pro.5560021103
Date:
28-Nov-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 120 a.a.
Key:    Secondary structure

 

 
DOI no: 10.1002/pro.5560021103 Protein Sci 2:1798-1810 (1993)
PubMed id: 7505680  
 
 
Knowledge-based model building of proteins: concepts and examples.
J.Bajorath, R.Stenkamp, A.Aruffo.
 
  ABSTRACT  
 
We describe how to build protein models from structural templates. Methods to identify structural similarities between proteins in cases of significant, moderate to low, or virtually absent sequence similarity are discussed. The detection and evaluation of structural relationships is emphasized as a central aspect of protein modeling, distinct from the more technical aspects of model building. Computational techniques to generate and complement comparative protein models are also reviewed. Two examples, P-selectin and gp39, are presented to illustrate the derivation of protein model structures and their use in experimental studies.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. A: Structure-basedsequencealignment of C-typelectin domains fP-selectin andthemannose-bindingprotein(MBP). Secondary-structureelments in MBP arelabeled.Residuescon- servedin MBP and P-slectin are boxedandresiduesconsrved in all selectins are shaded. This sequence-structurealignment provided the basis for comparative model building of the P-selectinligand-binding domain. B: Model structure of li- gand-bindng domain of P-selectin. The model,represented as a solid was ased on identified structural similar- ity to crystal structure of the C-typelectindomain of the rat mannose-bindingdomain, whichrevealed a previouslyunknown roteinfold.The iewis longa-helix 2, locatedbelow theloop regioncoloredinyellow. A conservedcalciumpositionisshwn in red.Analyisof the modelsuggeste a shallowdepression proximal to the conservedcalcium as a potentialligad-binding ite.Thisregion is flankedn the left by loop, colored yel- ow,with a five-residueinsertionreltive to the mannose-binding Residues the roposedligand-bindingregion of P-selectinweresubjected to ite-specificmutagenesisanalysis, the hypothesisregarding the location ofrsidues in P-selectincriticl inding to its cellularligand.Theresidues are shown in a colorcoded ashion:magenta,crucialfor binding; lavender,significant contribution to binding; blue, minorcon- tribution to binding. C: Assessentof the P-selectinmodelby comparison f 3D-profils of the MBPcrystal structure (rela- tive to the MBPsequence)andoftheP-selectinmodelstructure (relative to its sequence). The profiles were alculatedusing a 21-residuewindow for scoreaveraging. The calculatedZ-score for the MBPsequence and crystal structure is30.8, the Z-score for the P-selectinsequence and model is 34.9. No eg- ative valueswereobserved that ould ocalin- consistenciesin the structural odels. The analysissuggests n equivalentcompatibiltyofsequenceandstructure he model and the X-ray structure.
Figure 2.
Fi. 2. A: Model structure of he extracellular domain of gp39. The structureofthehomotrimer is in green. The y-axis is approximately to thethreefold molecular symmetry axis. he locations f site-specific natural gp39 mutants in three patients (C.D., A.Y. and J.W.) are These mutations im- pair thefunction of gp39 in these patients.One of thethree symmetry-related region n gp39 that correspond o the receptor- binding sites in tumor necrosis factor beta (TNFP) is in Locations of the three mutations shown heresuggests that residue changes may interfere with the binding ofgp39 to receptor CD40. B: Comparison of calculated 3D-profiles, a 21-residue window, forthe trimeric tumor necrosis fac- orapha (TNFa) crystal andthe trimeric gp39 model structure elative to their sequences. The calculated Z-scores the TNFa structure and sequence and forthe gp39 model and se- were 30.8 and 32.8,respectively. The analysis supports he proposed structral similarity of gp39 and
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1993, 2, 1798-1810) copyright 1993.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16281947 M.J.Conroy, P.A.Bullough, M.Merrick, and N.D.Avent (2005).
Modelling the human rhesus proteins: implications for structure and function.
  Br J Haematol, 131, 543-551.  
11250194 G.Mocz, and I.R.Gibbons (2001).
Model for the motor component of dynein heavy chain based on homology to the AAA family of oligomeric ATPases.
  Structure, 9, 93.
PDB code: 1hn5
  10850801 L.Cosenza, A.Rosenbach, J.V.White, J.R.Murphy, and T.Smith (2000).
Comparative model building of interleukin-7 using interleukin-4 as a template: a structural hypothesis that displays atypical surface chemistry in helix D important for receptor activation.
  Protein Sci, 9, 916-926.  
10861932 M.A.Bowen, A.A.Aruffo, and J.Bajorath (2000).
Cell surface receptors and their ligands: in vitro analysis of CD6-CD166 interactions.
  Proteins, 40, 420-428.  
10940251 M.A.Martí-Renom, A.C.Stuart, A.Fiser, R.Sánchez, F.Melo, and A.Sali (2000).
Comparative protein structure modeling of genes and genomes.
  Annu Rev Biophys Biomol Struct, 29, 291-325.  
11256577 M.C.Peitsch, T.Schwede, and N.Guex (2000).
Automated protein modelling--the proteome in 3D.
  Pharmacogenomics, 1, 257-266.  
10998071 M.Tamburrini, A.Riccio, M.Romano, B.Giardina, and G.di Prisco (2000).
Structural and functional analysis of the two haemoglobins of the antarctic seabird Catharacta maccormicki characterization of an additional phosphate binding site by molecular modelling.
  Eur J Biochem, 267, 6089-6098.  
  10091660 B.V.Reddy, H.A.Nagarajaram, and T.L.Blundell (1999).
Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins.
  Protein Sci, 8, 573-586.  
10470037 N.Guex, A.Diemand, and M.C.Peitsch (1999).
Protein modelling for all.
  Trends Biochem Sci, 24, 364-367.  
9692947 D.Kitchen, R.C.Hoffman, F.J.Moy, and R.Powers (1998).
Homology model for oncostatin M based on NMR structural data.
  Biochemistry, 37, 10581-10588.  
9636145 G.M.Lipkind, A.Zhou, and D.F.Steiner (1998).
A model for the structure of the P domains in the subtilisin-like prohormone convertases.
  Proc Natl Acad Sci U S A, 95, 7310-7315.  
9736622 L.Ribas de Pouplana, D.Buechter, N.Y.Sardesai, and P.Schimmel (1998).
Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domains.
  EMBO J, 17, 5449-5457.  
  9144767 H.Li, R.Tejero, D.Monleon, D.Bassolino-Klimas, C.Abate-Shen, R.E.Bruccoleri, and G.T.Montelione (1997).
Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1.
  Protein Sci, 6, 956-970.  
  9192474 J.Kubrycht, and K.Sigler (1997).
Animal membrane receptors and adhesive molecules.
  Crit Rev Biotechnol, 17, 123-147.  
9094331 R.Sánchez, and A.Sali (1997).
Advances in comparative protein-structure modelling.
  Curr Opin Struct Biol, 7, 206-214.  
  8845760 X.Chen, D.Whitmire, and J.P.Bowen (1996).
Xylanase homology modeling using the inverse protein folding approach.
  Protein Sci, 5, 705-708.  
7579655 A.Sali (1995).
Modeling mutations and homologous proteins.
  Curr Opin Biotechnol, 6, 437-451.  
  8563634 M.D.Toney, S.Pascarella, and D.De Biase (1995).
Active site model for gamma-aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities.
  Protein Sci, 4, 2366-2374.  
8589998 M.Karpusas, Y.M.Hsu, J.H.Wang, J.Thompson, S.Lederman, L.Chess, and D.Thomas (1995).
2 A crystal structure of an extracellular fragment of human CD40 ligand.
  Structure, 3, 1031-1039.
PDB code: 1aly
7777492 O.Fjellström, T.Olausson, X.Hu, B.Källebring, S.Ahmad, P.D.Bragg, and J.Rydström (1995).
Three-dimensional structure prediction of the NAD binding site of proton-pumping transhydrogenase from Escherichia coli.
  Proteins, 21, 91.  
  8535254 P.N.Lipke, M.H.Chen, H.de Nobel, J.Kurjan, and P.C.Kahn (1995).
Homology modeling of an immunoglobulin-like domain in the Saccharomyces cerevisiae adhesion protein alpha-agglutinin.
  Protein Sci, 4, 2168-2178.  
7765167 A.C.May, and T.L.Blundell (1994).
Automated comparative modelling of protein structures.
  Curr Opin Biotechnol, 5, 355-360.  
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.