4LEP | pdb_00004lep

Structural insights into substrate recognition in proton dependent oligopeptide transporters

PDB DOI: https://doi.org/10.2210/pdb4LEP/pdb

Classification: membrane protein, tranport protein
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2013-06-26 Released: 2013-07-10
Deposition Author(s): Guettou, F., Quistgaard, E.M., Tresaugues, L., Moberg, P., Jegerschold, C., Zhu, L., Jong, A.J., Nordlund, P., Low, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.325 (Depositor), 0.334 (DCC)
R-Value Work:
0.275 (Depositor), 0.279 (DCC)
R-Value Observed:
0.277 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural insights into substrate recognition in proton-dependent oligopeptide transporters.

Guettou, F., Quistgaard, E.M., Tresaugues, L., Moberg, P., Jegerschold, C., Zhu, L., Jong, A.J., Nordlund, P., Low, C.

(2013) EMBO Rep 14: 804-810

PubMed: 23867627 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/embor.2013.107
Primary Citation Related Structures:
4LEP

PubMed Abstract:
Short-chain peptides are transported across membranes through promiscuous proton-dependent oligopeptide transporters (POTs)--a subfamily of the major facilitator superfamily (MFS). The human POTs, PEPT1 and PEPT2, are also involved in the absorption of various drugs in the gut as well as transport to target cells. Here, we present a structure of an oligomeric POT transporter from Shewanella oneidensis (PepTSo2), which was crystallized in the inward open conformation in complex with the peptidomimetic alafosfalin. All ligand-binding residues are highly conserved and the structural insights presented here are therefore likely to also apply to human POTs.

Organizational Affiliation

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 114.91 kDa
Atom Count: 6,858
Modeled Residue Count: 907
Deposited Residue Count: 1,046
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton:oligopeptide symporter POT family	A, B	523	Shewanella oneidensis MR-1	Mutation(s): 0 Gene Names: SO_1277 Membrane Entity: Yes
UniProt
Find proteins for Q8EHE6 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EHE6 Go to UniProtKB: Q8EHE6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EHE6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AFS Query on AFS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	N-[(1R)-1-phosphonoethyl]-L-alaninamide C₅ H₁₃ N₂ O₄ P BHAYDBSYOBONRV-IUYQGCFVSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.325 (Depositor), 0.334 (DCC)
R-Value Work: 0.275 (Depositor), 0.279 (DCC)
R-Value Observed: 0.277 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.24	α = 90
b = 107.73	β = 90
c = 205.51	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SHARP	phasing
PHENIX	refinement
XDS	data reduction
anisotropy	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-10
Type: Initial release
Version 1.1: 2013-08-07
Changes: Database references
Version 1.2: 2013-10-23
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations