X-ray crystal structure, PDB

Fig. 4. Backscattered Raman and ROA spectra of the n-helical protein human serum albumin in H20 (top pair) and the /3-sheet protein jack bean concanavalin A in acetate buffer solution at pH 5.4, together with MOLSCRIPT diagrams (Kraulis, 1991) of their X-ray crystal structures (PDB codes lao6 and 2cna). 

Fig. 3.6 a Homology model of BaeL KS5 (Grey) overlaid onto DEBS KS3 X-Ray crystal structure (PDB 2Q03) showing high level of structural similarity, b Active site residues from BaeL KS5 and DEBS KS3 overlay. Spatial positioning of the residues is extremely similar for the model and the crystal structure... 

According to the PDB X-ray crystal structure 1 ao6, human serum albumin contains 69.2% o -helix and 1.7% 3io-helix, the rest being made up of turns and long loops. The amide I ROA couplet centered at 1650 cm-1 (Fig. 4), which is negative at low wavenumber and positive at high,... 

According to the PDB X-ray crystal structure 2cna, jack bean con-canavalin A contains 43.5% /1-strand, 1.7% a-helix, and 1.3% 3io-helix,... 

Figure 6.10 Secondary structure of the RNA 6 hammerhead ribozyme as found in the X-ray crystallographic structures PDB IHMH, IMME, 299D, 300D, 301D, 359D, 379D, and 488D. A modified RNA6 was used for crystal structures PDB INYI, and 1Q29.

Fig. 3. The X-ray crystal structure of the oxidized state of c3itochrome cdi nitrite reductase from P. pantotrophus (drawn from PDB entry 1 qks using MolScript 98, 99)).

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. 

Figure 2.4 X-ray crystal structures of different forms of MMOH from M. capsulatus (Bath) coordinates taken from PDB files 1FYZ (a) [59] and 1FZ6 (b) [60]. Coordinative bonds are represented bysolid linesand hydrogen bondsor weak bonds by dotted lines. Only the amino acid side-chains of the active site and coordinated aqua/hydroxido/methoxido ligands are shown. Hydrogen atoms have been omitted for clarity.

Figure 35. Global mapping of surface hydration dynamics of apoMb. Shown is the X-ray crystal structure of sperm whale myoglobin (PDB ID 1MBD) in the holo form with eight helices A—H. In apo form, parts of the structure are melted and they are shown in transparent gray. The 16 balls indicate positions of mutation with tryptophan one at a time.

Fig. 5 Top view of a representative G-quadruplex X-ray crystal structure (human telomeric DNA PDB ID 1KF1 [7]. Guanosine bases forming tetrads are at the center of the structure in this view...

Fig. 14. X-ray crystal structure of full-length yeast CCS [pdb code Iqup (Lamb et al., 1999)]. (a) One monomer of yCCS is in light gray and the other is in dark gray. The cysteine residues of the MXCXXC motif in domain 1 are labeled and form a disulfide bond in each subunit. Amino acid side chains that are important in the formation of the positive patch at the dimer interface (Arg-188 and Arg-217) and the solvent-exposed Trp-183 residues of loop 6 at the center of this patch are shown in ball-and-stick representation. Domain 3 is not visible in the crystal structure (see text), (b) Stereo view of the image in (a) rotated 90° in the horizontal plane of the page and then 90° counterclockwise around an axis perpendicular to the page. The side chains that form the putative ySODl interaction surface are represented as ball-and-stick. The cysteine residues of the domain 1 MXCXXC motif are also represented in ball-and-stick.

Figure 4 X-ray crystal structure of oxidized copper-containing nitrite reductase from Alcaligenes faecalis at 2.0 A resolution. Coordinates are from PDB entry 1AS7 ...

Figure 5 X-ray crystal structures of the Type 2 copper active site of nitrite reductase from Alcaligenes faecalis (a) oxidized and (b) nitrite-soaked. Panel (c) is a rotated view of (b) and shows the hydrogen-bonding network. Coordinates are from PDB entries 1AS7 and 1AS6 ...

Figure 3 The geometric arrangement of the redox active cofactors in Photosystem I and Photosystem II as given by the X-ray crystal structures PS I pdb entry IJBO (2) and PS II pdb entry 2AXT (3).

Page 1084 is adapted from crystallographic coordinates deposited with the Protein Data Barrk. PDB ID IPID. Brange, J., Dodson, G. G., Edwards, D. J., Holden, P. H., Whittingham, J. L., A Model of Insulin Fibrils Derived from the X-Ray Crystal Structure of a Monomeric Insulin (Despentapeptide Insulin). To be published. 

Fig. 1 (a) X-ray crystal structure of IL-2/IL-2Roe interface, with important IL-2Ra residues shown (b) X-ray crystal structure of SP4206 bound to IL-2. Key IL-2 residues are highlighted in both structures (pdb lz92, lpy2)... 

Fig. 1 X-ray crystal structure representations of well-known small molecule PPI targets, (a) p53 activation domain bound to MDM2 (PDB code lycr) (b) Bad BH3 domain bound to Bcl-xL (PDB code 2bzw) (c) HPV18 E2 activation domain bound to the helicase domain of El (PDB code ltue) (d) Smac bound to the XIAP-BIR3 domain (PDB code lg73) (e) HIV-1 gp41 core six-helix bundle with N and C regions labelled (PDB code li5x) (f) The c-Myc-Max DNA recognition complex (PDB code lnkp)...

The inhibitor has been described as exquisitely selective across a panel of over 200 kinases due to the specific nature of the interactions it makes with the inactive form of cMET. ARQ 197 has been extensively characterised as non-ATP competitive by biochemical, biophysical and structural studies. X-Ray crystal structure studies of ARQ 197 bound to cMET (PDB 3RHK) provides specific rationale for the selectivity profile of the compound, where the protein is seen in a conformation which has not been observed for other protein kinases. Figure 2.10 shows the overlay with ARQ 197 bound in cMET (brown) with a structure of cMET bound with ATP (3DKC,20 cyan). For ease of viewing only key side chains have been included and ATP has been removed. 

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