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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).
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M.A.Clark, R.A.Acharya, C.C.Arico-Muendel, S.L.Belyanskaya, D.R.Benjamin, N.R.Carlson, P.A.Centrella, C.H.Chiu, S.P.Creaser, J.W.Cuozzo, C.P.Davie, Y.Ding, G.J.Franklin, K.D.Franzen, M.L.Gefter, S.P.Hale, N.J.Hansen, D.I.Israel, J.Jiang, M.J.Kavarana, M.S.Kelley, C.S.Kollmann, F.Li, K.Lind, S.Mataruse, P.F.Medeiros, J.A.Messer, P.Myers, H.O'Keefe, M.C.Oliff, C.E.Rise, A.L.Satz, S.R.Skinner, J.L.Svendsen, L.Tang, K.van Vloten, R.W.Wagner, G.Yao, B.Zhao, B.A.Morgan. (2009). Design, synthesis and selection of DNA-encoded small-molecule libraries. Nat Chem Biol, 5, 647-654. [PubMed id: 19648931]
Figure 3.
(a) Selection output from DEL-A selections against Aurora A kinase. Low occurrence molecules (<4 copies) have been removed. Both selections show lines in the cycle 2 plane corresponding to 6-aminoquinoline. In method A, the line comprises 2-methoxyphenethylamine at cycle 3. In method B, there are two lines corresponding to 3,4-dimethoxyaniline and 4-pyrrolidinopiperidine at cycle 3. (b) Histograms showing the total occurrences of cycle 1 synthons after Aurora A selections. Using both methods, 7-AT is the highest occurring cycle 1 synthon. (c) Structures of synthesized compounds and their activity data. The compounds consist of members of both the 7-AT and the 6-aminoquinoline families. (d) Crystal structure of compound 10 bound to Aurora A kinase, showing the 2-fluorophenethylamine moiety exposed to solvent. Image created in Accelrys DS Viewer Pro 5.0.
Figure reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2009, 5, 647-654) copyright 2009.
PDB entries for which this is a key reference: 3ha6, 3ha8.
C.K.Kennaway, J.L.Benesch, U.Gohlke, L.Wang, C.V.Robinson, E.V.Orlova, H.R.Saibil, H.R.Saibi, N.H.Keep. (2005). Dodecameric structure of the small heat shock protein Acr1 from Mycobacterium tuberculosis. J Biol Chem, 280, 33419-33425. [PubMed id: 16046399]
Figure 2.
FIGURE 2. A, Acr2 (+His) nanoelectrospray mass spectrometry spectrum showing a range of different sized complexes. Analysis of the individual peaks by argon collision-induced dissociation reveals homo-oligomers consisting of even numbers of subunits from 12 up to 28, as well as other larger assemblies. B, nanoelectrospray mass spectrometry of Acr1 reveals the protein to exist as a dodecamer. The individual charge states of the peaks are labeled.
Figure 6.
FIGURE 6. A, surface representation of the three-dimensional map of Acr1 contoured at 2.2 , viewed down a 2-fold axis. The black line beneath is a 100 Å scale bar. B, model of Acr1 using the wheat -crystallin dimers. N-terminal residues 1-42 are omitted because of their unknown structure and likely flexibility. C-terminal residues 146-151 containing the IXI motif are shown in magenta, positioned as they are in the wheat crystal structure. These 6 residues occupy bulges in the density along the outer edges, seen most clearly at the top and bottom of this view. C, contacts between dimers are formed by the C-terminal extensions. Residues 146-151 (magenta sticks) can be seen binding to the edges of -sheets 3 and 7 of an -crystallin domain in an adjacent dimer (blue). The surface of the Acr1 EM reconstruction is shown, and the truncated end (residue 137) of the green -crystallin domain is shown colored red. The general direction of the path of the omitted residues is shown as a yellow dashed line. Figures were produced with Pymol (
Figures reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 33419-33425) copyright 2005.
PDB entries for which this is a key reference: 2byu.
S.Datta, C.Larkin, J.F.Schildbach. (2003). Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Structure, 11, 1369-1379. [PubMed id: 14604527]
Figure 7.
Figure 7. A Pocket within the Binding Surface of TraI36 Can Accommodate a DNA BaseShown is a model of Gua (shown as sticks) docked into a pocket of TraI36, shown as a molecular surface. The base fits well into the pocket, with little overlap in the van der Waals surfaces of the protein and the base, even without energy minimization of the complex or rearrangement of the protein or base. The surfaces of Arg201 (left) and Gln193 (right) are shown with carbons colored green, nitrogens colored blue, and oxygens colored red. The remainder of the binding pocket is largely hydrophobic. In this orientation, a hydrogen bond can be formed between the Gua O6 and the Arg side chain.
Figure reprinted by permission from Cell Press: Structure (2003, 11, 1369-1379) copyright 2003.
PDB entries for which this is a key reference: 1p4d.
PDB entries for which this is a secondary reference: 2a0i.
J.Koepke, E.M.Krammer, A.R.Klingen, P.Sebban, G.M.Ullmann, G.Fritzsch. (2007). pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. J Mol Biol, 371, 396-409. [PubMed id: 17570397]
Figure 2.
Figure 2. (a) Electron density around the distal and proximal QB positions in the structure of this work (pH 8, dark-adapted state; PDB entry 2j8c). The 0.2 and the 1σ levels of the density are depicted in blue and magenta wireframes, respectively. The models for the distal (orange) and the proximal (yellow) positions are shown as stick model. The two head-groups are tilted out of the image plane by about ±15°.
(b) Superposition of the two QB positions, color-coded in yellow, orange, and red, respectively, with the structures from Stowell et al. (PDB entries 1aig and 1aij) of the same state and at the same pH, shown in red. Hydrogen bonds to neighboring protein atoms are indicated by broken green lines, with their length given in Å.
(c) Schematic drawing of the QB movement. Distal position in black, hypothetical intermediate position in green, and proximal QB position in blue. Hydrogen bonds to the distal position are color-coded orange, to the intermediate position in red, and to the proximal QB position in magenta. The length of the total QB movement and the Cα–Cα distance are indicated by arrows.
Figure 6.
Figure 6. Proton-uptake upon reduction of Q[B] as calculated using the program GMCT. The total proton-uptake is shown by a continuous line and experimental values (taken from Tandori et al.^22) by black crosses with error bars. The contribution of Asp L213 (broken line) and the protonation of the semiquinone (dotted line) are shown additionally. The dash-dot line describes the proton uptake by the rest of the protein.
Figures reprinted by permission from Elsevier: J Mol Biol (2007, 371, 396-409) copyright 2007.
PDB entries for which this is a key reference: 2j8c, 2j8d, 2uws, 2uwt, 2uwu, 2uwv, 2uww, 2ux3, 2ux4, 2ux5, 2uxj, 2uxk, 2uxl, 2uxm.