7O82

The L-arginine/agmatine antiporter from E. coli at 1.7 A resolution

PDB DOI: https://doi.org/10.2210/pdb7O82/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli O157:H7
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2021-04-14 Released: 2021-09-08
Deposition Author(s): Jeckelmann, J.M., Ilgue, H., Kalbermatter, D., Fotiadis, D.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.203
R-Value Work: 0.195
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding.

Ilgu, H., Jeckelmann, J.M., Kalbermatter, D., Ucurum, Z., Lemmin, T., Fotiadis, D.

(2021) BMC Biol 19: 179-179

PubMed: 34461897 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12915-021-01102-4
Primary Citation of Related Structures:
7O82

PubMed Abstract:
The L-arginine/agmatine transporter AdiC is part of the arginine-dependent extreme acid resistance system of the bacterium Escherichia coli and its pathogenic varieties such as strain E. coli O157:H7. At the present time, there is a lack of knowledge concerning the role of water molecules and networks for the structure and function of AdiC, and solute transporters in general.

Organizational Affiliation

Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland.

Macromolecule Content

Total Structure Weight: 97.76 kDa
Atom Count: 7,053
Modelled Residue Count: 873
Deposited Residue Count: 906
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine/agmatine antiporter	A, B	453	Escherichia coli O157:H7	Mutation(s): 0 Gene Names: adiC, Z5717, ECs5097 Membrane Entity: Yes
UniProt
Find proteins for P60061 (Escherichia coli (strain K12)) Explore P60061 Go to UniProtKB: P60061
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60061
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BNG Query on BNG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	C [auth A], H [auth B], I [auth B]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B]	F [auth A], P [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain P [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B]	D [auth A], J [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	E [auth A] K [auth B] L [auth B] M [auth B] N [auth B] E [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]