Protein data bank files

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

HyperChem residue templates. HyperChem uses these templates when it reads a Protein Data Bank file or when you construct a molecule from residues. 

Protein data bank file numbers are indicated in parentheses. Surface areas were calculated using the Lee and Richards algorithm (1971) as described in the text. 

Brookhaven protein data bank files lead, arb9, and 8rxn. 

Figure 1. Three-dimensional structure of wild-type metmyoglobin on the basis of the Protein Data Bank file lYMB by S.V Evans and G.D. Brayer, J. Mol. Biol., 213 (1990) 885.

Also see color figure.) Complex of MHC class I proteins, HTLV-1 peptide (antigen) and TcR. The MHC class I proteins bind and present peptides that are synthesized inside the infected cell to T-cell receptors (TcRs) specific for the bound peptides. Interaction and stimulation of T-cell proliferation occurs with CDS positive, cytotoxic Tc cells. The figure is derived from the coordinates published in the Protein Data Bank file 1BD2. 

Also see color figure.) CD4 (cluster differentiation 4) protein. CD4 on T cells is a component of the MHC class II, TcR complex. Shown are the extracellular domains that consist of two immunoglobulin-like folds. The /3-sheet secondary structure is illustrated in one fold only the a-carbon backbone is shown in the other. The figure is derived from the coordinates published in the Protein Data Bank file 1WIO. 

CHAPTER 35, FIGURE 10 Binding of protein G (S. aureus) to an Fc fragment. Protein G binding mimics the Fc receptor binding of an Ig in the Ig Fc region. Protein G is used for purification of antibodies and in their capture in immunoassays. The figure is derived from the coordinates published in the Protein Data Bank file IFCC. 

Figure 4.1 The ATP-binding site of protein kinase A. Key polar interactions are shown by dashed lines. Drawn from the crystal structure in Protein Data Bank file latp. Mn2+ is replaced by Mg2+ in vivo.

Fig. 4.4 Schematic representation of rat ATM-FAAH, complexed with the irreversible inhibitor MAFP in green) (Protein Data Bank file 1MT5)...

Figure 6.3 Crystal structure of the mouse acetylcholinesterase-2 gallamine homodimer complex with 30% homology of 532 residues from the C-terminal cholinesterase part of human thyroglobulin (Tg). The three-dimensional structure of mouse acetylcholinesterase homodimer complex homological to part III of human Tg in Figure 6.1 was experimentally determined at a resolution of 2.20A using X-ray diffraction (Bourne et al., 2003 ExPASy access number P21836). A model of the molecule was constructed using CAChe software (Fujitsu Ltd, Japan) according to the XYZ coordinates from Protein Data Bank file (code 1 N5M.pdb).

Figure 4.30. Scheinatic representation of the three-dimensiortal atomic structure of rabbit skeletal actin (Kabsch. W., Mannherrz. H. 0., Shuck. D.. Pau E. F. and Holmes, K. C.. 1990. Nature. 347, 37-44) showing the position of the two residues, Lys-6l (acceptor) and Cys 374 (donor), that were modified. Because the three COOII-lerminal residues (involvuig Cys-374) are not reso ved in the crystal structure (Kabsch et al., 1990), the labeled position of the donor mo ecule should be taken as an approxunation. The four subdomains are also labeled (the coordinates were obtained from the Brookhaven Protein Data Bank, file lATN). Source Nyitral, M., Hiid, G.. Lakes. Zs and Somogyi, 6. 1998. Biophys. J. 74,2474 - 2481. Authorization of reprini accorded by the American Biophysical Society.

Fig. 4 Structure (right) and spectra (left) of open and closed conformations of myoglobin. Both x-ray diffraction and infrared absorption data were recorded on single crystals of MbCO at pH 6 (top) and pH 4 (bottom). Displacement of the distal histidine (blue) from the heme pocket in the open structure leads to a shift of the C-O stretch frequency from 1945 cm to 1966 cm and may facilitate entry and exit of small molecules. The solid curve represents the contribution of an individual protein conformer to the IR band, based on the 2.7 cm homogeneous linewidth expected from IR photon echo measurements.The heme is rendered in red. the bound CO in white, the distal histidine in blue, and the remainder of the protein in green. Atomic coordinates for structural models of MbCO at pH 6 and pH 4 were obtained from the Protein Data Bank files Ivxf and Ispe, respectively.(View this art in color at www.dekker.com.)...

In the first part of the work, computer modeling was used to develop molecular model of Microcystin-LR. An initial structure in low-energy conformation was found in the Protein Data Bank (file IQm.pdb) [73]. The molecule was corrected... 

Fig. 2 Comparison of the chlorophyll networks in PSI from cyanobacteria (Synechococcus elongatus) represented as black lines and the higher plants Pisum sativum var. alaska) represented as transparent gray bonds. The chlorophylls corresponding to the LHCI belt are not shown for plant PSI (see Figure 5). Figure made using Protein Data Bank files 1JBO and IQZV with the program VMD.

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