6ZGR | pdb_00006zgr

Crystal structure of a MFS transporter with bound 1-hydroxynaphthalene-2-carboxylic acid at 2.67 Angstroem resolution

PDB DOI: https://doi.org/10.2210/pdb6ZGR/pdb

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

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: 2.46 Å
R-Value Free:
0.255 (Depositor), 0.250 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 89.98 kDa
Atom Count: 5,779
Modeled Residue Count: 763
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0LNN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1HN (Subject of Investigation/LOI) Query on 1HN Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1-hydroxynaphthalene-2-carboxylic acid C₁₁ H₈ O₃ SJJCQDRGABAVBB-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: 2.46 Å
R-Value Free: 0.255 (Depositor), 0.250 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.553	α = 90
b = 199.572	β = 90
c = 62.468	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

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

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.