spacer
spacer

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.

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.

A maximum of 2 figures are selected from each reference. The selection is fully automatic, using an SVM trained to identify the most "interesting" figures in terms of structural or functional information content. However, in some cases, the figures may correspond to the article authors' preferred choice.

To get a new random selection, press the "Renew" button below.

T.Izard, M.C.Lawrence, R.L.Malby, G.G.Lilley, P.M.Colman. (1994). The three-dimensional structure of N-acetylneuraminate lyase from Escherichia coli. Structure, 2, 361-369. [PubMed id: 8081752]
Figure 2.
Figure 2. Stereo Cα trace of the Neu5Ac lyase monomer, viewed down the β -barrel axis from its carboxy-terminal end. Every tenth Cα is labelled. Figure 2. Stereo Cα trace of the Neu5Ac lyase monomer, viewed down the β -barrel axis from its carboxy-terminal end. Every tenth Cα is labelled. (Figure produced using MOLSCRIPT [[3]10].)
Figure 3.
Figure 3. Schematic drawing of the secondary structural elements of Neu5Ac lyase viewed down the β -barrel axis from its carboxy- terminal end. The putative catalytic residue Lys165 (see text) is shown in ball-and-stick representation. Figure 3. Schematic drawing of the secondary structural elements of Neu5Ac lyase viewed down the β -barrel axis from its carboxy- terminal end. The putative catalytic residue Lys165 (see text) is shown in ball-and-stick representation. (Figure produced using MOLSCRIPT [[3]10].)
Figures reprinted by permission from Cell Press: Structure (1994, 2, 361-369) copyright 1994.
PDB entries for which this is a key reference: 1nal.
PDB entries for which this is a secondary reference: 1fdy, 1fdz, 1hl2.
M.K.Swan, D.Bastia, C.Davies. (2006). Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication. Proc Natl Acad Sci U S A, 103, 18481-18486. [PubMed id: 17124167]
Figure 3.
Fig. 3. The secondary structure of plotted against its sequence using the same coloring as Fig. 2. Dashed lines indicate those regions of the protein that were not included in the final model because of incomplete electron density. Important residues are colored according to the following scheme: blue (and italic), residues that contact DNA; red, sites of high-copy-number mutants (P106L, F107S, and P113S; ref. 22); orange, the mutation (P42L) that causes a defect in DNA looping (24); green, sites of double mutations that lower binding to DnaB helicase (this study); and purple, mutants that are defective for replication but still bind DNA (this study).
Figure 4.
Fig. 4. The interaction of with iteron DNA. The protein is shown in ribbon format with residues that lie close to DNA in bond form in the NTD of (a) and the CTD (b). Potential hydrogen bonds are shown as dashed lines.
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (2006, 103, 18481-18486) copyright 2006.
PDB entries for which this is a key reference: 2nra.
R.Graeff, Q.Liu, I.A.Kriksunov, M.Kotaka, N.Oppenheimer, Q.Hao, H.C.Lee. (2009). Mechanism of cyclizing NAD to cyclic ADP-ribose by ADP-ribosyl cyclase and CD38. J Biol Chem, 284, 27629-27636. [PubMed id: 19640843]
Figure 1.
Crystal structure of the complex of cyclase with ribo-2′F-NAD.a, chemical structure of the substrate ribo-2′F-NAD and the reactions catalyzed by CD38 and the cylase. b, crystal structure of the cyclase dimer with the intermediates at each of the active sites of the monomer. The color scheme for the secondary structures is: red, α-helix; yellow, β-sheet; gray, coil. The color scheme for the residues is: cyan, Tyr-81; beige, Phe-174; blue, Glu-179; magenta, Glu-98; purple, Phe-175. The intermediates are colored by their elements: green, carbon; red, oxygen; orange, phosphorus; blue, nitrogen; light green, fluorine. c, stereo view of the folded conformation with electron density from an omit F[o] − F[c] map contoured at 2.7 σ and shown as blue wire mesh. Other color schemes are the same as in b. The average B-factor is 76 Å^2 for the folded intermediate.
Figure 2.
Two conformations of the intermediate from ribo-2′F-NAD.a, the extended conformation. The orange dashed line shows that the distance between the adenine and Tyr-81 is 4.0 Å. Phe-175 is colored in purple. Other color schemes are as in Fig. 1b. b, the folded conformation. The magenta dashed line shows that the distance between the adenine and Phe-174 is 4.1 Å. c, surface view of the active site pocket with the two conformations of intermediate superimposed. The folded conformation is colored by its elements as in Fig 1a. The extended conformation is colored beige. Surface color is as follows: deep blue, Phe-174; cyan, Tyr-81; red, Glu-179; white, all other residues. d, rotational conversion between the two conformations. The folded conformation is brightly colored by its elements as in Fig. 1a. The distance between N1 of the adenine is 5.2 Å from Glu-179 in this conformation. The extended conformation is lightly colored by its elements.
Figures reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 27629-27636) copyright 2009.
PDB entries for which this is a key reference: 3i9o.
M.S.Dunstan, D.Guhathakurta, D.E.Draper, G.L.Conn. (2005). Coevolution of protein and RNA structures within a highly conserved ribosomal domain. Chem Biol, 12, 201-206. [PubMed id: 15734647]
Figure 1.
Figure 1. Secondary and Tertiary Structures of the 58 Nucleotide L11 Binding Domain rRNA
Figure 3.
Figure 3. Interactions in the Ch-like rRNA-L11(C76) Complex
Figures reprinted by permission from Cell Press: Chem Biol (2005, 12, 201-206) copyright 2005.
PDB entries for which this is a key reference: 1y39.
spacer
spacer