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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.

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.

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N.Tanaka, M.Nakanishi, Y.Kusakabe, K.Shiraiwa, S.Yabe, Y.Ito, Y.Kitade, K.T.Nakamura. (2004). Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum. J Mol Biol, 343, 1007-1017. [PubMed id: 15476817]
Figure 7.
Figure 7. Summary of the inhibitory activities of 2-functional-group-introduced noraristeromycin against HsSAHH, PfSAHH, and mutant PfSAHH (Cys59Thr).
Figure 8.
Figure 8. Surface representation of the active site of PfSAHH. A molecule of 2-F-noraristeromycin (2-F-NAM) is modeled into the Ado-binding site of PfSAHH. Superposition was done with respect to the adenine rings of Ado and 2-F-NAM. The carbon atoms and a fluorine atom are shown in pink and green, respectively. A surface depression that exists specifically in PfSAHH, but not in HsSAHH, is indicated by stars.
Figures reprinted by permission from Elsevier: J Mol Biol (2004, 343, 1007-1017) copyright 2004.
PDB entries for which this is a key reference: 1v8b.
PDB entries for which this is a secondary reference: 3ond, 3one, 3onf, 4lvc.
S.R.Hubbard. (1997). Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog. EMBO J, 16, 5572-5581. [PubMed id: 9312016]
Figure 1.
Figure 1 Electron density map of the active site of IRK3P. Stereo view of a 2F[o] -F[c] map computed at 1.9 resolution and contoured at 1.2 . Superimposed is the refined atomic model. Carbon atoms are yellow, oxygen atoms red, nitrogen atoms blue, phosphate atoms purple, and sulfur atoms green. The red spheres represent water molecules and the white spheres represent Mg2+ ions. Figure prepared with SETOR (Evans, 1993).
Figure 2.
Figure 2 Overall view of IRK3P and comparison with IRK. (A) Ribbon diagram of the IRK3P structure. The -helices are shown in red, the -strands in blue, the nucleotide-binding loop in yellow, the catalytic loop in orange, the activation loop in green, AMP-PNP in black and the peptide substrate in pink. The termini are denoted by N and C. (B) Superposition of the C-terminal lobes of IRK and IRK3P. The backbone representation of IRK/IRK3P is colored orange/green, with the activation loop colored red/blue. The axis (black) and arrow (blue) specify the rotation required to align the N-terminal -sheet of IRK with that of IRK3P. (C) Superposition of the -sheets in the N-terminal lobes of IRK and IRK3P. The backbone representation and carbon atoms of IRK/IRK3P are colored orange/green, oxygen atoms are red and nitrogen atoms are blue. (A) and (C) prepared with RIBBONS (Carson, 1991), (B) with GRASP (Nicholls et al., 1991).
Figures reprinted from Open Access publication: EMBO J (1997, 16, 5572-5581) copyright 1997.
PDB entries for which this is a key reference: 1ir3.
PDB entries for which this is a secondary reference: 1gag.
L.Zhang, J.A.Doudna. (2002). Structural insights into group II intron catalysis and branch-site selection. Science, 295, 2084-2088. [PubMed id: 11859154]
Figure 2.
Fig. 2. Crystal structure of d56-TR. (A) Stereo ribbon diagram representation of the crystal structure of d56-TR. Green helix, domain 5; blue helix, domain 6; gray helix, tetraloop receptor; gold spheres, magnesium ions. Difference Fourier maps contoured at 5 are superimposed with the structure to show cobalt hexammine (in pink) and manganese ion (in cyan) binding sites. The branch-point A880 is marked with an asterisk (*) and the conserved AGC sequence (816 to 818) in domain 5 is also labeled. (B) Observed secondary structure of d56-TR. Color coding and sequence numbering are the same as in Fig. 1B. Predicted metal ion-binding sites, orange arrows; base stacking, gray dashed line. (C) Part of the 2F[o] - F[c ]map, contoured at 1.5 , around the domain 6 branch-point region; the structural model of domain 6 is in blue. The stacking residues U881, A880 (and its 2'-OH group), and A862 are labeled. (D) Close-up view of domain 6 structure around the branch point. The structural model of domain 6 is represented by blue ribbons except for residues A880, U881, and A862. A880 and U881 form the double-bulged branch-point structure and stack with A862. The branch-point adenosine (A880) is labeled and its 2'-OH group is shown in red. Fig. 2, A, C, and D are created using RIBBONS (37).
Figure 3.
Fig. 3. Chemical probing of wild-type d56. (A) Secondary structure of wild-type d56. New secondary structure of wild-type d56 is indicated with a double-bulged branch point; uridines in domain 6 are labeled. (B) Summary of CMCT probing. Normalized CMCT modification levels are shown in bar graph; residue numbers for uridines in domain 6 are indicated.
Figures reprinted by permission from the AAAs: Science (2002, 295, 2084-2088) copyright 2002.
PDB entries for which this is a key reference: 1kxk.
T.Hibi, H.Nii, T.Nakatsu, A.Kimura, H.Kato, J.Hiratake, J.Oda. (2004). Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis. Proc Natl Acad Sci U S A, 101, 15052-15057. [PubMed id: 15477603]
Figure 3.
Fig. 3. Stereoview of the residues surrounding the Cys-analog moiety of sulfoximine 2, showing the distances between the ligands. The molecular surface around the Cys-binding site is drawn in white.
Figure 5.
Fig. 5. Superimposition of residues 238-251, including the switch loop. The loop's hinge residues, Gly-240 and Leu-249, are labeled.
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (2004, 101, 15052-15057) copyright 2004.
PDB entries for which this is a key reference: 1v4g, 1va6.
PDB entries for which this is a secondary reference: 2d32, 2d33.
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