Protein Data Bank PDB

PDB file. pdb Protein Data Bank file format for 3D stmcture information on proteins and polynucleotides nmm.rcsb.org 53... 

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/home/home.do is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 4.5 include the facihty to visualize imported data however, two free software programs operate well in this regard. One is MDL Chime described previously in this section. Chime, a chemical structure visualization plug-in for Internet Explorer and Netscape Communicator, supports a wide variety of molecule coordinate formats, including PDB (protein data bank), Molfile (from ISIS/Draw), MOP (MOPAC input hies), and GAU (Gaussian Input hies). 

Homologous proteins of the CYP superfamily with known structure serve as the templates for homology modeling. The sequence similarities and/or identities between the template and target proteins should be as high as possible. Several search methods such as FASTA (40) or BLAST (41) are available to retrieve template homologs from the PDB (Protein Data Bank) (42). 

The X-ray crystal structures shown in this article were created with CambridgeSoft s ChemSD Pro 5.0 using coordinates obtained from the source, the CSD (Cambridge Structural Database) or the PDB (Protein Data Bank), or those determined by Paul D. Robinson at Southern Illinois University (SIU) in collaboration with the author. Most of the author s work on boron heterocycles first at SIU and more recently at SRI International (the nonprofit research institute formerly known as the Stanford Research Institute) was funded by NIH grant GM448I9. 

PCMCIA (Personal Computer Memory Card International Association) pdb (Protein Data Bank) format PDF (portable document format)... 

Abbreviations Cdk, q din-dependent kinase pRb, retinoblastome protein PDB, Protein Data Bank MW, molecular weight ... 

Figure 20.4 X-ray structures of the binding sites of the Abl kinase/imatinib and cytochrome P450 3A4 /erythromycin complexes (PDB Protein Data Bank). The amino acids located within 4A of ligands are depicted. The hydrogen bonding interactions are shown by dashed lines, and the amino acids participating in hydrogen-bonding interactions are labeled in bold. The images were produced with Pymol (DeLano Scientific LLC). See color plates.

Abbreviations used in table MC - Monte Carlo aa - amino acid vdW - van der Waals potential Ig - immunoglobulin or antibody CDR - complementarity-determining regions in antibodies RMS -root-mean-square deviation r-dependent dielectric - distance-dependent dielectric constant e - dielectric constant MD - molecular dynamics simulation self-loops - prediction of loops performed by removing loops from template structure and predicting their conformation with template sequence bbdep - backbone-dependent rotamer library SCMF - self-consistent mean field PDB - Protein Data Bank Jones-Thirup distances - interatomic distances of 3 Ca atoms on either side of loop to be modeled. 

Cell dimensions are in angstroms, cell angles are in degrees. The crystal structures have been determined at room tempera ture if not stated explicitly. NR, Not reported. = 2 /i - intensity measurement, and (/) is the average intensity for this reflections the sum is over all reflections, i is a conventional crystallographic agreement factor. PDB, Protein Data Bank. 

PDB = Protein Data bank PLP = pyridoxal 5 phosphate E. coli = Escherichia coii. 

PDB PROTEIN DATA BANK AT THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS (RCSB)... 

PDB protein data bank NMR nuclear magnetic resonance. 

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