6GHJ

PepTSt in complex with tripeptide Phe-Ala-Gln

PDB DOI: https://doi.org/10.2210/pdb6GHJ/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Streptococcus thermophilus LMG 18311, synthetic construct
Expression System: Escherichia coli, synthetic construct
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2018-05-08 Released: 2018-09-19
Deposition Author(s): Martinez Molledo, M., Quistgaard, E.M., Loew, C.
Funding Organization(s): European Union, Swedish Research Council

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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wwPDB Validation 3D Report Full Report

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

PubMed: 30194725 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 58.33 kDa
Atom Count: 4,005
Modelled Residue Count: 460
Deposited Residue Count: 486
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Di-or tripeptide:H+ symporter	A	483	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: dtpT, stu0970 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5M4H8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHE-ALA-GLN	B	3	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
78M Query on 78M Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain V [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain V [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain V [auth A]	J [auth A], L [auth A], V [auth A]	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE C₁₈ H₃₄ O₄ BJMLBVHMHXYQFS-JJEJIETFSA-N		Interactions Focus chain J [auth A] Focus chain L [auth A] Focus chain V [auth A] Interactions & Density Focus chain J [auth A] Focus chain L [auth A] Focus chain V [auth A]
78N Query on 78N Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	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		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

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 = 101.55	α = 90
b = 108.22	β = 90
c = 111.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

Martinez Molledo, M.

Quistgaard, E.M.

Loew, C.

Funding Organization	Location	Grant Number
European Union		653706
Swedish Research Council		621-2013-5905

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

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Help and Resources

6GHJ

PepTSt in complex with tripeptide Phe-Ala-Gln

Tripeptide binding in a proton-dependent oligopeptide transporter.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2