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PDBsum entry 1dlp

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protein Protein-protein interface(s) links
Sugar binding protein PDB id
1dlp
Jmol
Contents
Protein chains
233 a.a. *
221 a.a. *
Waters ×67
* Residue conservation analysis
PDB id:
1dlp
Name: Sugar binding protein
Title: Structural characterization of the native fetuin-binding protein scilla campanulata agglutinin (scafet): a novel two-domain lectin
Structure: Lectin scafet precursor. Chain: a, b, c, d, e, f
Source: Hyacinthoides hispanica. Organism_taxid: 81759. Other_details: protein was extracted from the bulbs of this plant
Biol. unit: Hexamer (from PQS)
Resolution:
3.30Å     R-factor:   0.189     R-free:   0.293
Authors: L.M.Wright,C.D.Reynolds,P.J.Rizkallah,A.K.Allen, E.J.M.Vandamme,M.J.Donovan,W.J.Peumans
Key ref:
L.M.Wright et al. (2000). Structural characterisation of the native fetuin-binding protein Scilla campanulata agglutinin: a novel two-domain lectin. FEBS Lett, 468, 19-22. PubMed id: 10683433 DOI: 10.1016/S0014-5793(00)01109-1
Date:
11-Dec-99     Release date:   10-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9ZP48  (Q9ZP48_HYAHI) -  Lectin SCAfet (Fragment)
Seq:
Struc:
265 a.a.
233 a.a.
Protein chains
Pfam   ArchSchema ?
Q9ZP48  (Q9ZP48_HYAHI) -  Lectin SCAfet (Fragment)
Seq:
Struc:
265 a.a.
221 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0014-5793(00)01109-1 FEBS Lett 468:19-22 (2000)
PubMed id: 10683433  
 
 
Structural characterisation of the native fetuin-binding protein Scilla campanulata agglutinin: a novel two-domain lectin.
L.M.Wright, C.D.Reynolds, P.J.Rizkallah, A.K.Allen, E.J.Van Damme, M.J.Donovan, W.J.Peumans.
 
  ABSTRACT  
 
The three-dimensional structure of a 244-residue, multivalent, fetuin-binding lectin, SCAfet, isolated from bluebell (Scilla campanulata) bulbs, has been solved at 3.3 A resolution by molecular replacement using the coordinates of the 119-residue, mannose-binding lectin, SCAman, also from bluebell bulbs. Unlike most monocot mannose-binding lectins, such as Galanthus nivalis agglutinin from snowdrop bulbs, which fold into a single domain, SCAfet contains two domains with approximately 55% sequence identity, joined by a linker peptide. Both domains are made up of a 12-stranded beta-prism II fold, with three putative carbohydrate-binding sites, one on each subdomain. SCAfet binds to the complex saccharides of various animal glycoproteins but not to simple sugars.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Vacant Fo-Fc electron density in the region of (A) 114 Asn and (B) 129 Tyr of subunit A. The linker peptide 114 Asn-125 Asn, as well as the residues 126 Ser, 127 Ile, 128 Leu were excluded from the model at this stage of the analysis. (C) Modelling of part of the 11-residue linker peptide into the difference density. The figures were produced with O [15].
Figure 4.
Fig. 4. Superposition of SCAman (light gray) onto SCAfet (black) in the region of subdomain I showing the shorter loop with the four-residue deletion for SCAfet compared to the corresponding loop in SCAman and its position relative to the linker peptide. The figure was produced with MOLSCRIPT [19].
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2000, 468, 19-22) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17609367 S.Naithani, T.Chookajorn, D.R.Ripoll, and J.B.Nasrallah (2007).
Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain.
  Proc Natl Acad Sci U S A, 104, 12211-12216.  
16843894 N.E.ZióÅ‚kowska, B.R.O'Keefe, T.Mori, C.Zhu, B.Giomarelli, F.Vojdani, K.E.Palmer, J.B.McMahon, and A.Wlodawer (2006).
Domain-swapped structure of the potent antiviral protein griffithsin and its mode of carbohydrate binding.
  Structure, 14, 1127-1135.
PDB codes: 2gty 2guc 2gud 2gue 2gux
16183566 E.G.De Mejía, and V.I.Prisecaru (2005).
Lectins as bioactive plant proteins: a potential in cancer treatment.
  Crit Rev Food Sci Nutr, 45, 425-445.  
  16508116 U.V.Katre, S.M.Gaikwad, S.S.Bhagyawant, U.D.Deshpande, M.I.Khan, and C.G.Suresh (2005).
Crystallization and preliminary X-ray characterization of a lectin from Cicer arietinum (chickpea).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 141-143.  
15649901 W.Liu, N.Yang, J.Ding, R.H.Huang, Z.Hu, and D.C.Wang (2005).
Structural mechanism governing the quaternary organization of monocot mannose-binding lectin revealed by the novel monomeric structure of an orchid lectin.
  J Biol Chem, 280, 14865-14876.
PDB codes: 1xd5 1xd6
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