Protein databank

Different methods have been devised to represent proteins. A structure for porcine pancreatic procolipase is reported in the Protein Databank, as determined by NMR spectroscopy. Many such structures are reported without the hydrogen atoms, since their positions often cannot be determined experimentally. Most MM packages will add hydrogens. Figure 1.18 gives the hydrogen-free procolipase structure in line representation. 

Fig. 5. Side-by-side stereo presentation of a ribbon diagram of the Lck SH2 domain, Protein Databank entry code 1BHF.PDB [118]... 

Fig. 6. Schematic diagram of the peptide-protein interaction mode as seen in the crystallo-graphically refined structured of the Lck SH2 domain-peptide complex, Protein Databank entry code 1 LKK.PDB. The residues directly engaged in intramolecular hydrogen bonds (dotted lines) are labeled explicitly... 

Fig. 8. Lck SH2 domain-peptide complex (Ac-cmF-Glu-Glu-Ile-OH, 12) revealing the twopronged plug engaging a two-holed socket 1 binding mode, reminiscent of the majority of SH2 domains (Protein Databank entry code 1BHF.PDB [118]). The protein is depicted in a Connolly surface mode, the ligand is given in a ball-and-stick representation. The cmF residue is deeply buried in its binding pocket (left)...

Table 3.1 Statistical data from the Protein Databank (PDB) at present [17]...

Rasmol It was one of the first Protein Databank (PDB) compatible viewers available as freeware. Upgrades have now been stopped, but the program is still widely available. Versions exist for both PC and Mac. 

Figure 10.4. The D. vulgaris Rbo dimer (Coehlo et al. 1997). Spheres, iron atoms in centers I and II. The model was generated via RASMOL (Sayle and MUner-White 1995) and coordinates from IDFX in the Protein Databank.

Figure 10.6. Structural features of D. vulgaris Rbr (deMare et al. 1996). A, Rbr subunit with protein backbone and iron atoms (spheres). B, Diiron-oxo site with amino acid side chain ligands. Models generated via RASMOL (Sayle and Milner-White 1995) and coordinates from IRYT in the Protein Databank.

McKay and co-workers determined the X-ray crystallographic structure of a hammerhead RNA-DNA ribozyme complex at 2.6-A resolution in 1994, deposited in the Protein Databank (PDB) as IHMH. The substrate DNA strand ensured that the complex would remain in the ground state since the DNA 2 -deoxy position could not undergo the cyclization/cleavage reaction. 

Through this modification, they hoped to capture a later conformational intermediate poised to form an inline transition state. The technique used was that of time-resolved crystallography, one that has successfully captured protein intermediates (see Section 3.7.2.3). The data determining the crystal structure has been deposited in the Protein Databank as PDB 379D. 

Abola EB, Sussman JL,PrUuskyJ, Manning NO (1997) Protein databank archives of three-dimensional macromolecular structures. In Carter CW Jr, Sweet RM (eds) Methods in enzymology, vol 277. Academic Press, San Diego, pp 556-571... 

The Worldwide Protein Databank Berman HM, Heirrlck K, Nakamura H (2003) Nat Struct Biol 10 980. http //www.wwpdb.org/... 

Overview of AAH crystal structures deposited in the protein databank from human (h), rat (r), Chromobacterium violaceum (cv), Colwellia psychrerythraea... 

Cover concept by eStudio Calamar Steinen using a background picture from The Protein Databank (1 Kzu). Courtesy of Dr. Antoine M. van Oijen, Department of Molecular Physics, Huygens Laboratory, Leiden University, The Netherlands. Reprinted with permission from Science 285 (1999) 400-402 ("Unraveling the Electronic Structure of Individual Photosynthetic Pigment-Protein Complexes", by A. M. van Oijen et al.) Copyright 1999, American Association for the Advancement of Science. 

Fig. 3. Gallery of Ga effector GAP complexes. The Ga subunits, colored according to the scheme in Fig. 1, are similarly oriented in the four panels. Effector domains are colored pale green, and GAP domains light tan Panel A, complex among Gas GTPyS and the VCi and IIC2 domains of mammalian mAC. The latter is shown bound to forskolin and a nonhydrolyzable analogue of ATP (protein Databank ID 1CJT)...

Data formats in the Brookhaven Protein Databank have become an intensively discussed topic in the last few years. The original PDB file format [17] was created in the late 1970s and maintained by the Research Collaboratory for Structural Bioinformatics [13]. In order to improve the organization of bibliographic... 

M. Hendlich, F. Rippmann, G. Barnick-el. BALI automatic assignment of bond and atom types for protein ligands in the brookhaven protein databank. /. Chem. Inf. Comput. Sci., 37, 774-778, 1997. 

By extracting the structure from a (PDB) file of a ligand-protein complex deposited at the Protein Databank. 

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