Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes x-ray diffraction data identifying the structure of Mtb Lpd bound to 010705. The main summary display for this entry includes information on the experimental method and validation, macromolecules, small molecules, funding information and version history. Data is provided for download as FASTA sequence format, the Protein Data Bases own PDB format, crystallographic information file (.cif), XML, the EM map, as well as the full validation file in either PDF or XML formats. Additionally, the PDB provides embedded visualization software to display a 3D view of the protein: PDB's Mol* viewer, NGL viewer, and JSmol. PDB provides protein family and gene product annotations, additional details about the experiment parameters, a Protein Feature Viewer (in the Sequence tab) which displays all available features and alignments of known polymer instances, and a genome view which provides graphical summaries of the correspondences between PDB Entity sequences and genomes.

Subject of Study

Mycobacterium tuberculosis

Subject(s)

Dihydrolipoamide Dehydrogenase

Oxidoreductases

Access via PDB
Research Collaboratory for Structural Bioinformatics Protein Data Base
Accession #: 7KMY
Access Restrictions: Free to All
Access Instructions: The RCSB Protein Data Base provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA). Sequence, protein structure, EM, and other data can be downloaded in formats specific to the data they contain.
DOI: 10.2210/pdb7KMY/pdb
Associated Publications: Ginn J, Jiang X, Sun S, et al. Whole cell active inhibitors of mycobacterial lipoamide dehydrogenase afford selectivity over the human enzyme through tight binding interactions. ACS Infectious Diseases. 2021; 7(2):435-444.
Data Type: Genomic
Equipment Used: APS (Advanced Photon Source) Beamline 24-ID-C
Sector 24 utilizes canted insertion devices to provide two independent x-ray sources, one for a variable energy beamline 24-ID-C and another for a fixed energy beamline 24-ID-E (Se peak). Both beamlines are optimized to address challenging cases in macromolecular crystallography such as large complex molecular assemblies, poorly diffracting crystals and microcrystals by providing extremely stable and intense x-ray beams with beam sizes ranging from 5 to 70 microns. The 24-ID-C beamline is equipped with an ALS-style sample auto-mount robotic system for increased productivity and a mini-kappa goniometer head for crystal alignment.

DECTRIS PILATUS3 S 6M
Hybrid Photon Counting X-ray detector
Software Used: HKL-2000
The HKL-2000 program package is based on the extended versions of Denzo, XdisplayF and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important elements are: simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc.

JSmol
HTML5 modality of the Jmol open-source Java viewer for chemical structures in 3D

Mol*
Plugin created by the Protein Data Base to visualize protein structures

NGL
NGL Viewer is a web application for molecular visualization.

PDB EXTRACT
Program Suite contains tools and examples for extracting mmCIF data from structure determination applications.

PHENIX
A software suite for the automated determination of molecular structures using X-ray crystallography and other methods

SCALEPACK
The scaling and merging of different data sets as well as the global refinement of crystal parameters (postrefinement) is performed by Scalepack
Dataset Format(s): PDF, XML, FASTA, PDB, CIF, MTZ, DSN6
Data Tool(s): X-ray crystallography (XRC)
Dataset Size: 627 KB (FASTA), 615 (PDB)

Data Catalog Record Updated: 2021-07-27

Structure of Mtb Lpd bound to 010705