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A random selection of article figures used in PDBsum

The 4 randomly selected references below show some of the article figures used in PDBsum. Each reference may relate to one or more PDBsum entries and may be one of the following types:

key reference - cited in the JRNL records in the corresponding PDB file,
secondary reference - listed in the REMARK records of the corresponding PDB file, or
added reference - either suggested by the author(s) or obtained from the journal in question (eg Acta Cryst D lists related PDB codes on its contents pages).

Note that only figures from the key and added references are displayed on the given entry's PDBsum page. Figures from the secondary references only appear on the entry's references page, which is reached via the "References" link on the left.

The figures used are either from Open Access publications or from journals for which we have obtained permission from the publishers to use their copyright material.

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F.A.Saul, B.Vulliez-le Normand, F.Lema, G.A.Bentley. (1998). Crystal structure of a dominant B-cell epitope from the preS2 region of hepatitis B virus in the form of an inserted peptide segment in maltodextrin-binding protein. J Mol Biol, 280, 185-192. [PubMed id: 9654443]



	Figure 1. Figure 1. Schematic view of MalE-B363 in stereo; (a) molecule 1 and (b) molecule 2. The genetically inserted peptide at the carboxy terminus of the hybrid is shown in red and the bound molecule of maltose is shown in blue. Illustrations were produced by MOLSCRIPT [Kraulis 1991].		Figure 2. Figure 2. Stereo view of the electron density corresponding to the genetically inserted peptide in MalE-B363 (a) from residues 364(i) to 383(i) in molecule 1 and (b) from residues 364(i) to 141(e) in molecule 2. Contours are drawn at the 1 r.m.s. level of a (2F[o]−F[c]) electron density map. No significant electron density was observed for the epitope insertion in molecule 3.

PDB entries for which this is a key reference: 1a7l.

H.Steuber, M.Zentgraf, A.Podjarny, A.Heine, G.Klebe. (2006). High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group. J Mol Biol, 356, 45-56. [PubMed id: 16337231]



	Figure 6. Figure 6. Refinement model of the ALR2 binding pocket at 0.95 Å resolution occupied by the pyridazinone inhibitor 6 shown in blue. For clarity, the specificity pocket is represented only in the open conformation. Amino acid residues are shown in orange, water molecules are indicated as red spheres. F[o] -F[c] density contoured at 3.5 s is shown in blue. It clearly depicts the positions of the inhibitor atoms.		Figure 7. Figure 7. The F[o] -F[c] difference map next to residues in the catalytic center provides evidence for the protonation states of Tyr48, Lys77, His110, Trp111 and the pyridazinone moiety. Furthermore, a water molecule is indicated mediating a hydrogen bond network to His110 Nd2, Lys77 CO and the backbone NH groups of His46 and Val47. H bonds are shown as dotted green lines and the electron density corresponding to the hydrogen atoms is contoured in blue at 1.8 s. The inhibitor is shown in blue. The representation presents the binding pocket in two orientations: (a) the H bond interactions between the inhibitor and Tyr48 OH, His 110Ne2 and Trp111 Ne1; (b) clearly shows the threefold protonated Lys77 side-chain nitrogen atom involved in an H-bond network to Tyr48 OH, Asp43 Od2 and Cys44 CO.

PDB entries for which this is a key reference: 1z89, 1z8a.

B.P.Hudson, M.A.Martinez-Yamout, H.J.Dyson, P.E.Wright. (2004). Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d. Nat Struct Mol Biol, 11, 257-264. [PubMed id: 14981510]



	Figure 3. Figure 3. Solution structure of the RNA complex of TIS11d. (a) Stereo view of the best 20 structures superposed on backbone heavy atoms in ordered regions of the protein and RNA. The protein backbone is blue, the RNA backbone red, and RNA bases yellow. For clarity, only ordered regions of TIS11d (residues 153 -217) and RNA bases U2 -U9 are shown. (b) Ribbon representation of a single structure, in the same orientation as in a, showing the location and coordination of zinc in each of the fingers. Colors are the same as in a, with the addition of green side chains for the zinc-coordinating ligands. (c) Backbone superposition of the structure ensembles of fingers 1 and 2. Finger 1 (Arg153 -Phe180) is dark blue (backbone), green (zinc-coordinating side chains) and red (intercalating aromatic rings); the bound RNA (U6, A7, U8, U9) is orange. The corresponding colors for finger 2 are light blue, yellow, pink and yellow. Figures were generated using MolMol50.		Figure 4. Figure 4. Molecular recognition of RNA by TIS11d and hydrogen bonding between TIS11d and RNA. (a) Molecular contact surface of a representative TIS11d TZF structure generated in GRASP51 showing surface topology. Green denotes convex surfaces. The locations of the (R/K)YKTEL motifs that form the U6 and U2 binding pockets are indicated. (b) Stereo view showing hydrogen-bonding interactions between finger 1 and the 3' UAUU subsite. The protein backbone is light blue, the RNA backbone and bases pale yellow, and the intercalating aromatic side chains green. Each of the intermolecular hydrogen bonds is designated with a number and identified by a red line and colored atoms (red, oxygen; white, hydrogen; blue, nitrogen). (c) Schematic figure summarizing hydrogen-bonding interactions (dotted lines) with each of the bases in both subsites of the ARE. The hydrogen bond numbers for finger 1 in part b are shown. Panels a and b were generated using MolMol50.

PDB entries for which this is a key reference: 1rgo.

G.Katona, R.C.Wilmouth, P.A.Wright, G.I.Berglund, J.Hajdu, R.Neutze, C.J.Schofield. (2002). X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution. J Biol Chem, 277, 21962-21970. [PubMed id: 11896054]



	Figure 1. Fig. 1. Structure and electron density for the acyl-intermediate near the substrate binding cleft at 0. 95-Å resolution. A, 2F[obs] F[calc] electron density map contoured to 1.7 (blue) and 4.0 (gold). The blue contour level was chosen such that atoms with 60% occupancy become visible in the active site. The structural model for the enzyme moiety is green, with the exception of the oxygen and nitrogen atoms of the catalytic histidine and serine, which are colored red and blue, respectively. The acyl-peptide moiety is colored orange. B, least square superposition of the 0.95-Å acyl-intermediate structure (cyan) and the 1.1-Å native elastase structure (green).		Figure 2. Fig. 2. Detailed view of the ester bond and the oxy-anion hole. A, stereo representation illustrating the degree of pyramidal distortion of the ester bond. The transparent plane passes through the carbonyl oxygen of the ester bond, the C[ ]of Ile-7, and O[ ]of Ser-195. The displacement of the carbonyl carbon of the ester bond from this plane is 0.05 Å. B, ball-and-stick representation of the enzymatic ester bond within the oxy-anion hole. The naming convention in Table III is used to identify atoms. C, ball-and-stick representation of the ethyl-acetate structure, providing an example of a small molecular ester.

PDB entries for which this is a key reference: 1gvk.
PDB entries for which this is a secondary reference: 2bda, 2bdb, 2bdc.