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PDBsum Gallery

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.

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R.J.Mallis, B.W.Poland, T.K.Chatterjee, R.A.Fisher, S.Darmawan, R.B.Honzatko, J.A.Thomas. (2000). Crystal structure of S-glutathiolated carbonic anhydrase III. FEBS Lett, 482, 237-241. [PubMed id: 11024467]
Figure 4.
Fig. 4. Stereo, surface representation of S-glutathiolated CAIII in the vicinity of the Cys183 adduct. The two conformers of the Cys183 adduct are represented by wireframe models. The disulfide bonds between GSH1 and Cys183 are shown as thin black lines. The view is approximately the same as that in Fig. 3B. The image was generated using MolMol [28]. A: Conformation 1 of the Cys183–GSH1 adduct. This is the same conformation of Cys183 as is found in the reduced bovine CAIII structure [27]. B: Conformation 2 of Cys183–GSH1 adduct.
Figure 5.
Fig. 5. Electrostatic and solvent-accessible surface representation of CAIII in stereo. Dark gray coloration represents a positive charge, light gray a negative charge and white a neutral charge. The position of S^γ of the GSH adducts are indicated by white balls. The lower portion of the figure shows the electrostatic surface of CAIII when the cysteines are in conformation 1. This is the same conformation as that of the reduced bovine CAIII model [21]. The upper portion of the figure shows the surface when Cys183 is in conformation 2. The electrostatic and surface calculations were carried out using MolMol [28], which utilizes the algorithm of Nicholls and Honig [29].
Figures reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2000, 482, 237-241) copyright 2000.
PDB entries for which this is a key reference: 1flj.
M.Coles, T.Diercks, J.Liermann, A.Gröger, B.Rockel, W.Baumeister, K.K.Koretke, A.Lupas, J.Peters, H.Kessler. (1999). The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Curr Biol, 9, 1158-1168. [PubMed id: 10531028]
Figure 1.
Figure 1. Folding topology of VAT-N. The characteristic H^α–H^α and H^N–H^N NOE connectivities used to determine the arrangement of β-strands are shown (black and white arrows, respectively). The data show β bulges in strands β7 and β10. Loops indicated by dashed lines are not to scale. The psi-loops in the amino-terminal subdomain are in bold. N, amino terminus; C, carboxyl terminus.
Figure 6.
Figure 6. GRASP [32] and [33] surface of VAT-N. Two views are shown; the left panels are equivalent to those shown in Figure 4, that is, looking at the top of the hexameric ring, whereas the right panels represent a view looking from within the ring towards the cleft between the two subdomains. The upper panels are coloured according to electrostatic potential, with values ranging from −7.0 (red) to 7.0 (blue) in units of k[B]T, and bottom panels according to the hydrophobicity of the underlying residues (hydrophobic, polar, positively charged and negatively charged residues are shown in white, green, blue and red, respectively). The strong positive charge of the top surface of the molecule is evident. This is mainly due to the many arginine residues concentrated on this face of the protein. In contrast, the inner surface of the protein is relatively uncharged or negatively charged.
Figures reprinted by permission from Cell Press: Curr Biol (1999, 9, 1158-1168) copyright 1999.
PDB entries for which this is a key reference: 1cz4, 1cz5.
J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson. (2003). Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure, 11, 121-127. [PubMed id: 12517346]
Figure 3.
Figure 3. DNA Polymerase b Ternary Complex with 8-OxodG-dCTP(A) 2F[o] - F[c] electron density map contoured at 1 s (black), superimposed on the refined model. Additionally, a difference map was calculated, omitting O8 and contoured at 3.3 s. Negative density (red) is visible at the 8-oxy position of the template base, demonstrating unbiased evidence of the presence of the additional oxygen. The ternary complex with an 8-oxodG template base is very similar to the previously determined ternary complex containing undamaged deoxyguanine paired with ddCTP [12]. The modified guanine is in the standard anti conformation, and dCTP is bound with a coordinating Mg2+ atom (data not shown).(B) Comparison of the 5'-phosphate backbone conformation of 8-oxodG relative to that observed in the structure of pol b with an unmodified deoxyguanine in the polymerase active site (orange) [12]. The presence of the sharp bend along with limited enzyme contacts with this phosphate enables flipping of the phosphate away from the carbonyl oxygen at C8 of 8-oxodG. The backbone a torsion angle (O3'-P-O5'-C5') of the templating guanine is altered 184 when a carbonyl group is introduced at C8. In addition, the Lys280 side chain position, but not that of Asp276, is altered in the presence of 8-oxodG.
Figure reprinted by permission from Cell Press: Structure (2003, 11, 121-127) copyright 2003.
PDB entries for which this is a key reference: 1mq2, 1mq3.
D.J.Ericsson, A.Kasrayan, P.Johansson, T.Bergfors, A.G.Sandström, J.E.Bäckvall, S.L.Mowbray. (2008). X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation. J Mol Biol, 376, 109-119. [PubMed id: 18155238]
Figure 1.
Fig. 1. Overall structure. In each panel, CalA is colored beginning with blue at the N terminus, going through the rainbow to red at the C terminus. (a) A C^α trace is shown in divergent stereo view. N and C termini are labeled. Every 20th residue is numbered, and the two disulfide bonds are indicated by C1 and C2. The active-site residues Ser184, Asp334 and His366 are shown as ball-and-stick representations with atomic coloring, together with a space-filling model of the observed molecule of PEG. (b) A cartoon representation is shown from the same view. N and C termini are labeled. (c) In a topology diagram, β-sheets are displayed as arrows and α-helices as rectangles, and labeled to define the naming convention. Active-site residues are indicated with black stars.
Figure 6.
Fig. 6. Proposed CalA reaction mechanism. In step 1 of the reaction, an ester substrate enters the active site and is subjected to nucleophilic attack by Ser184, which is itself activated by proton abstraction by the His366/Asp334 pair. The resulting tetrahedral intermediate is stabilized by interactions with the backbone nitrogen of Gly185, and the protonated side chain of Asp95. Similar involvement of an aspartic acid residue in the oxyanion hole is observed among the mammalian prohormone convertases,^45 as well as in α/β hydrolases.^42^,^43 In step 2, His366 releases its proton to the alcohol product as the tetrahedral intermediate collapses. The alcohol leaves the site, and a water molecule enters (step 3). After being activated by the histidine/aspartate pair, the water molecule attacks the acyl enzyme to generate a second tetrahedral intermediate, which then collapses to release the carboxylate product (step 4).
Figures reprinted by permission from Elsevier: J Mol Biol (2008, 376, 109-119) copyright 2008.
PDB entries for which this is a key reference: 2veo.
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