6ZGU | pdb_00006zgu

Crystal structure of a MFS transporter with bound 3-(2-methylphenyl)propanoic acid at 2.41 Angstroem resolution

PDB DOI: https://doi.org/10.2210/pdb6ZGU/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Syntrophobacter fumaroxidans MPOB
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2020-06-19 Released: 2021-10-20
Deposition Author(s): Kalbermatter, D., Bosshart, P., Bonetti, S., Fotiadis, D.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.244 (Depositor)
R-Value Work:
0.215 (Depositor)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The making of a potent L-lactate transport inhibitor

Bosshart, P.D., Kalbermatter, D., Bonetti, S., Fotiadis, D.

(2021) Commun Chem 4: 128

DOI: https://doi.org/10.1038/s42004-021-00564-5

Macromolecule Content

Total Structure Weight: 89.93 kDa
Atom Count: 5,822
Modeled Residue Count: 768
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate transporter	A, B	420	Syntrophobacter fumaroxidans MPOB	Mutation(s): 0 Gene Names: Sfum_3364 Membrane Entity: Yes
UniProt
Find proteins for A0LNN5 (Syntrophobacter fumaroxidans (strain DSM 10017 / MPOB)) Explore A0LNN5 Go to UniProtKB: A0LNN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0LNN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
02Q (Subject of Investigation/LOI) Query on 02Q Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	3-(2-methylphenyl)propanoic acid C₁₀ H₁₂ O₂ JIRKNEAMPYVPTD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.244 (Depositor)
R-Value Work: 0.215 (Depositor)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.048	α = 90
b = 199.703	β = 90
c = 61.616	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Kalbermatter, D.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_184980

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.