6GHJ

PepTSt in complex with tripeptide Phe-Ala-Gln


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Tripeptide binding in a proton-dependent oligopeptide transporter.

Martinez Molledo, M.Quistgaard, E.M.Low, C.

(2018) FEBS Lett 592: 3239-3247

  • DOI: https://doi.org/10.1002/1873-3468.13246
  • Primary Citation of Related Structures:  
    6GHJ

  • PubMed Abstract: 

    Proton-dependent oligopeptide transporters (POTs) are important for the uptake of di-/tripeptides in many organisms and for drug transport in humans. The binding mode of dipeptides has been well described. However, it is still debated how tripeptides are recognized. Here, we show that tripeptides of the sequence Phe-Ala-Xxx bind with similar affinities as dipeptides to the POT transporter from Streptococcus thermophilus (PepT S t ). We furthermore determined a 2.3-Å structure of PepT S t in complex with Phe-Ala-Gln. The phenylalanine and alanine residues of the peptide adopt the same positions as previously observed for the Phe-Ala dipeptide, while the glutamine side chain extends into a hitherto uncharacterized pocket. This pocket is adaptable in size and can likely accommodate a wide variety of peptide side chains.


  • Organizational Affiliation

    Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Di-or tripeptide:H+ symporter483Streptococcus thermophilus LMG 18311Mutation(s): 0 
Gene Names: dtpTstu0970
Membrane Entity: Yes 
UniProt
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Explore Q5M4H8 
Go to UniProtKB:  Q5M4H8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M4H8
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PHE-ALA-GLN3synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
78M
Query on 78M

Download Ideal Coordinates CCD File 
J [auth A],
L [auth A],
V [auth A]
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
78N
Query on 78N

Download Ideal Coordinates CCD File 
I [auth A]
K [auth A]
M [auth A]
N [auth A]
O [auth A]
I [auth A],
K [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
C18 H34 O4
BJMLBVHMHXYQFS-XZVRFQMRSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
F [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.55α = 90
b = 108.22β = 90
c = 111.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union653706
Swedish Research Council621-2013-5905

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description