1SLF

APOSTREPTAVIDIN, PH 5.6, TWO MOLECULES OF (SO4)2 BOUND AT THE BIOTIN BINDING SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence

Katz, B.A.

(1995) Biochemistry 34: 15421-15429

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The streptavidin-bound crystal structures of two disulfide-bridge cyclic peptides (cyclo-Ac-[CHPQGPPC]-NH2 and cyclo-Ac-[CHPQFC]-NH2) and of a linear peptide (FSHPQNT) were determined, as well as the structure of apostreptavidin (streptavidin-sulfate ...

    The streptavidin-bound crystal structures of two disulfide-bridge cyclic peptides (cyclo-Ac-[CHPQGPPC]-NH2 and cyclo-Ac-[CHPQFC]-NH2) and of a linear peptide (FSHPQNT) were determined, as well as the structure of apostreptavidin (streptavidin-sulfate). Both the linear and disulfide-bridged cyclic peptides studied share a common HPQ conformation and make common interactions with streptavidin, although significant differences in structures and interactions occur for flanking residues among the complexes. The conformation of the linear peptide in the crystal structure of streptavidin-FSHPQNT was found to differ from that in the same complex published [Weber, P. C., Pantoliano, M. W., & Thompson, L. D. (1992) Biochemistry 31, 9350-9354]. In the present investigation, the HPQNT portion of the ligand is well-defined with some density defining the Phe, whereas in the investigation of Weber et al. only the HPQ segment of the bound peptide could be interpreted. Both bound cyclic peptides adopt a beta-turn involving an H-bond between the His main chain carbonyl and the main chain amide NH of the i+3 residue. In the streptavidin-bound cyclo-Ac-[CHPQFC]-NH2 structure, there is an additional H-bond, indicative of alpha-helix, between the main chain His carbonyl and the main chain C-terminal Cys amide NH group. Binding interactions for both cyclic and linear peptides include direct H-bonds, H-bonds mediated by tightly bound water molecules, and hydrophobic interactions. The above structures and that of streptavidin-biotin in the literature are compared and discussed in the context of structure-based ligand design.


    Organizational Affiliation

    Arris Pharmaceutical Corporation, South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STREPTAVIDIN
B, D
135Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 95.430α = 90.00
b = 106.120β = 90.00
c = 47.540γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
X-PLORphasing
SADIEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-03-10 
  • Released Date: 1996-04-03 
  • Deposition Author(s): Katz, B.A.

Revision History 

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance