PDBsum entry 1vwf

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Complex (biotin-binding protein/peptide) PDB id
Protein chain
121 a.a. *
Waters ×228
* Residue conservation analysis
PDB id:
Name: Complex (biotin-binding protein/peptide)
Title: Streptavidin complexed with cyclo-ac-[chpqgppc]-nh2 monomer,
Structure: Streptavidin. Chain: b. Engineered: yes. Peptide ligand containing hpq. Chain: p. Engineered: yes
Source: Streptomyces avidinii. Organism_taxid: 1895.
Biol. unit: Octamer (from PDB file)
1.92Å     R-factor:   0.191     R-free:   0.236
Authors: B.A.Katz,R.T.Cass
Key ref:
B.A.Katz and R.T.Cass (1997). In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0. J Biol Chem, 272, 13220-13228. PubMed id: 9148939 DOI: 10.1074/jbc.272.20.13220
03-Mar-97     Release date:   18-Mar-98    
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Protein chain
Pfam   ArchSchema ?
P22629  (SAV_STRAV) -  Streptavidin
183 a.a.
121 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.272.20.13220 J Biol Chem 272:13220-13228 (1997)
PubMed id: 9148939  
In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0.
B.A.Katz, R.T.Cass.
The pH dependences of the affinities for streptavidin of linear and cyclic peptide ligands containing the HPQ sequence discovered by phage display were determined by plasmon resonance measurements. At pH values ranging from 3.0 to 9.0, the Kd values for Ac-AEFSHPQNTIEGRK-NH2, cyclo-Ac-AE[CHPQGPPC]IEGRK-NH2, and cyclo-Ac-AE[CHPQFC]IEGRK-NH2, were determined by competition, and those for cyclo-[5-S-valeramide-HPQGPPC]K-NH2 were determined directly by equilibrium affinity measurements. The Kd values of the ligands increase by an average factor of 3.0 +/- 0.8 per decrease in pH unit between pH approximately 4.5 and pH approximately 6.3. Below pH approximately 4.5 there is a smaller increase in Kd values, and above pH approximately 6.3 the Kd values become relatively pH-independent. We determined the crystal structures of complexes of streptavidin with cyclo-[5-S-valeramide-HPQGPPC]K-NH2 at pH 1.5, 2.5, 3.0, and 3.5, with cyclo-Ac-[CHPQFC]-NH2 at pH 2.0, 3.0, 3.6, 4.2, 4.8, and 11.8, with cyclo-Ac-[CHPQGPPC]-NH2 at pH 2.5, 2.9, and 3.7, and with FSHPQNT at pH 4.0 and compared the structures with one another and with those previously determined at other pH values. At pH values from 3.0 to 11.8, the electron density for the peptide His side chain is strong, flat, and well defined. A hydrogen bond between the Ndelta1 atom of the His and the peptide Gln amide group indicates the His of the bound peptide in the crystals is uncharged at pH >/= 3.0. By determining selected structures in two different space groups, I222 with two crystallographically inequivalent ligand sites and I4122 with one site, we show that below pH approximately 3.0, the pKa of the bound peptide His in the crystals is influenced by crystal packing interactions. The presence of the Ndelta1His-NGln hydrogen bond along with pH dependences of the peptide affinities suggest that deprotonation of the peptide His is required for high affinity binding of HPQ-containing peptides to streptavidin both in the crystals and in solution.
  Selected figure(s)  
Figure 3.
Fig. 3. A, low energy hydrogen bonding network for Trp79, Thr90, a bound water, and the peptide Gln. B, alternate, higher energy, hydrogen bonding scheme for these groups.
Figure 4.
Fig. 4. Hydrogen bonding network in streptavidin-FSHPQNT. Protein residues are white, peptide ligand is yellow-orange, and^ bound waters are light blue.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 13220-13228) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16699183 I.Le Trong, D.G.Aubert, N.R.Thomas, and R.E.Stenkamp (2006).
The high-resolution structure of (+)-epi-biotin bound to streptavidin.
  Acta Crystallogr D Biol Crystallogr, 62, 576-581.
PDB codes: 2f01 2gh7
16923020 S.C.Meyer, T.Gaj, and I.Ghosh (2006).
Highly selective cyclic peptide ligands for NeutrAvidin and avidin identified by phage display.
  Chem Biol Drug Des, 68, 3.  
15324809 L.Chen, A.J.Zurita, P.U.Ardelt, R.J.Giordano, W.Arap, and R.Pasqualini (2004).
Design and validation of a bifunctional ligand display system for receptor targeting.
  Chem Biol, 11, 1081-1091.  
12021449 D.Legendre, B.Vucic, V.Hougardy, A.L.Girboux, C.Henrioul, J.Van Haute, P.Soumillion, and J.Fastrez (2002).
TEM-1 beta-lactamase as a scaffold for protein recognition and assay.
  Protein Sci, 11, 1506-1518.  
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