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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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S.Graziani, J.Bernauer, S.Skouloubris, M.Graille, C.Z.Zhou, C.Marchand, P.Decottignies, H.van Tilbeurgh, H.Myllykallio, U.Liebl. (2006). Catalytic mechanism and structure of viral flavin-dependent thymidylate synthase ThyX. J Biol Chem, 281, 24048-24057. [PubMed id: 16707489]
Figure 1.
FIGURE 1. PBCV-1 ThyX structure. A, ribbon representation of the PBCV-1 ThyX monomer. B, ribbon representation of the ThyX homotetramer; each monomer is colored differently. The four bound FAD molecules are shown as sticks. The monomer highlighted in green is related to the representation in A by a 90° rotation along the x axis. C, stereo view representation of the comparison of the ThyX FAD binding mode. PBCV-1 and MtbThyX are colored yellow and green, respectively. For clarity, only PBCV-1 ThyX numbering is indicated. As TmThyX FAD binding mode is closely similar to that of MtbThyX, it has been omitted. Phosphorous atoms from FAD are colored black. For clarity, the labels corresponding to residues from monomer B are underlined. D, stereo view representation of the superposition of the active sites from PBCV-1 (yellow), MtbThyX (green), and TmThyX (gray). For clarity, only PBCV-1 ThyX numbering is indicated. Phosphorous atoms from FAD are colored black. E, ribbon representation of the hydrogen bonding pattern responsible for the binding of the FAD isoalloxazine moiety. Residues from monomers A, A', and B are colored gray, yellow, and green, respectively.
Figure 6.
FIGURE 6. Mapping of the ThyX residues involved in catalysis. PBCV-1 and MtbThyX are colored yellow and gray, respectively. PBCV-1 ThyX residues whose mutation completely affects NAD(P)H oxidation or methyl transfer are represented in red and orange, respectively. The two positions, His^79 and His^177 for which substitution by lysine or glutamine has either dramatic or no effect on ThyX activity, are colored in light blue. The bromine atom from BrdUMP is colored in purple. For clarity, only PBCV-1 ThyX numbering is indicated. Phosphorous atoms from FAD and BrdUMP are colored in black.
Figures reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 24048-24057) copyright 2006.
PDB entries for which this is a key reference: 2cfa.
P.Sliz, R.Engelmann, W.Hengstenberg, E.F.Pai. (1997). The structure of enzyme IIAlactose from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system. Structure, 5, 775-788. [PubMed id: 9261069]
Figure 8.
Figure 8. Stereo view representation of a modelled enzyme IIA-HPr complex. With knowledge of the phosphorylation site, the family of NMR structures of P-HPr (PDB code 1PFH coloured in red) was docked into the crystallographic model of enzyme IIA. The P-HPr ensemble of structures was rotated around the apical axis (red line) to minimize clashes and short contacts between the two proteins. Residues possibly involved in electrostatic interaction are Glu64[IIA] and Arg17[HPr]. Sidechains of His78[IIA], His82[IIA] and P-His15[HPr] are displayed and coloured by atom type.
Figure reprinted by permission from Cell Press: Structure (1997, 5, 775-788) copyright 1997.
PDB entries for which this is a key reference: 1e2a.
PDB entries for which this is a secondary reference: 2e2a.
D.C.Yeh, L.M.Parsons, J.F.Parsons, F.Liu, E.Eisenstein, J.Orban. (2005). NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog. Protein Sci, 14, 424-430. [PubMed id: 15632286]
Figure 1.
Figure 1. Summary of structure and dynamics data for HI0004. (A) Distribution of long range (filled columns), medium range (shaded columns), and sequential (unfilled columns) restraints per residue. (B) Plot of 15N-R[2] relaxation parameters for each residue. (C) The steady-state {1H}-15N nuclear Overhauser effect (NOE). (D) Backbone RMSDs (N, C[ ], CO) per residue with the secondary structure shown beneath the graph.
Figure 2.
Figure 2. Comparison of the HI0004 NMR structure with the AQ_1354 X-ray structure. (A) Backbone superposition of the 20 lowest energy structures of HI0004 determined by NMR spectroscopy. (B) Ribbon diagram of HI0004 with annotated secondary structure elements. The 5-helix is highlighted in yellow, and the conserved histidine side chains, H114 and H118 in 4 and H124 in the 4- 5 loop, are shown in blue. (C) X-ray structure of AQ_1354 (Oganesyan et al. 2003) showing the position of the three conserved histidine residues, H115, H119, and H125, in blue. The 5-helix is highlighted in yellow.
Figures reprinted by permission from the Protein Society: Protein Sci (2005, 14, 424-430) copyright 2005.
PDB entries for which this is a key reference: 1xax.
L.M.Podust, Y.Kim, M.Arase, B.A.Neely, B.J.Beck, H.Bach, D.H.Sherman, D.C.Lamb, S.L.Kelly, M.R.Waterman. (2003). The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems. J Biol Chem, 278, 12214-12221. [PubMed id: 12519772]
Figure 3.
Fig. 3. Superimposition of structures. A, superimposition between two CYP154C1 molecules in an asymmetric unit. B, superimposition between CYP154C1 and EryF. Superimposition was performed by using SWISS PDB VIEWER (50) according to an algorithm implemented in the program. The diagrams here and in Figs. 4 and 5 were prepared using SETOR (61). CYP154C1 is shown in gray with the FG region highlighted in blue, the BC loop and the B' helix in violet, and the -sheet 1 in magenta. EryF (Protein Data Bank code 1OXA) is in green with the BC loop highlighted in orange. The EryF substrate 6-deoxyerythronolide B is denoted by gray balls. Heme is in red.
Figure 4.
Fig. 4. Putative substrate-binding site of CYP154C1. For a better view of the cleft entrance, the CYP154C1 molecule in Fig. 3 was rotated toward the viewer approximately along the horizontal axis in the plane of the drawing. Residues building the left wall of the binding site cleft are from the BC loop (violet), and residues building the right wall are from the FG region (blue) and the I helix (green). Residues lining the back side of the cleft (gray) are from the last turn within -sheet 3 and from the junction between the K helix and the strand 1-5.
Figures reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 12214-12221) copyright 2003.
PDB entries for which this is a key reference: 1gwi.