9OLR | pdb_00009olr

Crystal structure of D59C MelB st bound with alpha-methyl galactoside (aMG)

PDB DOI: https://doi.org/10.2210/pdb9OLR/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli 0.1197
Mutation(s): Yes

Deposited: 2025-05-12 Released: 2026-02-04
Deposition Author(s): Guan, L., Hariharan, P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.68 Å
R-Value Free:
0.331 (Depositor), 0.330 (DCC)
R-Value Work:
0.295 (Depositor), 0.297 (DCC)
R-Value Observed:
0.297 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Allosteric effects of the coupling cation in melibiose transporter MelB

Hariharan, P., Shi, Y., Amirhossein, B., Liang, R., Viner, R., Guan, L.

(2026) Elife

DOI: https://doi.org/10.7554/elife.108335.2

Macromolecule Content

Total Structure Weight: 54.29 kDa
Atom Count: 3,570
Modeled Residue Count: 453
Deposited Residue Count: 485
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Melibiose permease	A	485	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1 Gene Names: melB, STM4299
UniProt
Find proteins for P30878 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P30878 Go to UniProtKB: P30878
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30878
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMG (Subject of Investigation/LOI) Query on AMG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	methyl alpha-D-galactopyranoside C₇ H₁₄ O₆ HOVAGTYPODGVJG-PZRMXXKTSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.68 Å
R-Value Free: 0.331 (Depositor), 0.330 (DCC)
R-Value Work: 0.295 (Depositor), 0.297 (DCC)
R-Value Observed: 0.297 (Depositor)

Diffraction Data: https://doi.org/10.1038/s42003-021-02462-x

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.496	α = 90
b = 127.496	β = 90
c = 106.039	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM153222

Revision History (Full details and data files)

Version 1.0: 2026-02-04
Type: Initial release

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.