Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes x-ray diffraction data identifying the monoclonal antibody targeting Matrix metalloproteinase 7. The main summary display for this entry includes information on the experimental data, validation, macromolecules included in the deposit, version history and funding identification. Data is provided for download as FASTA sequence format, the Protein Data Bases own PDB format, crystallographic information file (.cif), XML, DSN6 Maps, MTZ Map Coefficients, 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

Mus musculus

Subject(s)

Antibodies, Monoclonal

Matrix Metalloproteinase 7

Access via PDB
Research Collaboratory for Structural Bioinformatics Protein Data Base
Accession #: 6FBJ
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/pdb6FBJ/pdb
Associated Publications: Mohan V, Gaffney J, Solomonov I, et al. Conformation-specific inhibitory anti-MMP-7 monoclonal antibody sensitizes pancreatic ductal adenocarcinoma cells to chemotherapeutic cell kill. Cancers. 2021; 13(7):1679.
Data Type: Analytical Chemistry
Equipment Used: RIGAKU RAXIS IV++
X-ray area detector for macromolecular crystallography

RIGAKU RU300
The RU-300 uses a high-power X-ray source along with a diffracted beam monochromator for rapid, high-quality data collection from polycrystalline samples
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.

PHASER
Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods.

REFMAC5
REFMAC now has two ‘modes’: REVIEW which only checks and updates the input model to establish that the geometric restraints can be properly set up, and the standard REFINE mode documented in keywords.
Dataset Format(s): PDF, XML, FASTA, PDB, CIF, MAP, MTZ
Data Tool(s): X-ray crystallography (XRC)
Dataset Size: 553 KB (FASTA), 144 KB (PDB)

Data Catalog Record Updated: 2021-07-06

monoclonal antibody targeting Matrix metalloproteinase 7