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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.Bochtler, L.Ditzel, M.Groll, R.Huber. (1997). Crystal structure of heat shock locus V (HslV) from Escherichia coli. Proc Natl Acad Sci U S A, 94, 6070-6074. [PubMed id: 9177170]
Figure 5.
Fig. 5. Overlay of HslV (red) with the T. acidophilum -subunit (green) with bound calpain inhibitors. The secondary structural elements are labeled.
Figure 6.
Fig. 6. Overlay of one hexameric ring of HslV (red) with one heptameric ring of T. acidophilum -subunits (green).
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (1997, 94, 6070-6074) copyright 1997.
PDB entries for which this is a key reference: 1ned.
PDB entries for which this is a secondary reference: 1do0, 1do2, 1doo, 1e94.
N.Yamaji, L.Dai, K.Sugase, M.Andriantsiferana, T.Nakajima, T.Iwashita. (2004). Solution structure of IsTX. A male scorpion toxin from Opisthacanthus madagascariensis (Ischnuridae). Eur J Biochem, 271, 3855-3864. [PubMed id: 15373831]
Figure 9.
Fig. 9. Electrostatic potential surfaces of IsTX (A) and HsTX1 (B). The charge was assigned to normally ionizable residues (Asp, Glut, Lys and Arg). Negatively charged regions are shown in red and positively charged regions in blue. The figure was generated using MOLMOL.
Figure 10.
Fig. 10. Comparison of structures of IsTX and HsTX1. Selected sidechains are shown for IsTX (yellow) and HsTX1 (dark green) and labeled for IsTX (black) and HsTX1 (green). Conserved residues (Met29, Asn30, Arg31) surrounding Lys27 (A) and nonconserved residues and bulky C-terminal residues of IsTX (B).
Figures reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2004, 271, 3855-3864) copyright 2004.
PDB entries for which this is a key reference: 1wmt.
S.Bencharit, C.L.Morton, E.L.Howard-Williams, M.K.Danks, P.M.Potter, M.R.Redinbo. (2002). Structural insights into CPT-11 activation by mammalian carboxylesterases. Nat Struct Biol, 9, 337-342. [PubMed id: 11967565]
Figure 1.
Figure 1. Crystal structure of rabbit liver carboxylesterase. a, Two-step activation of the anticancer topoisomerase I poison CPT-11 to SN-38 (the active metabolite) and 4-piperidino-piperidine (4PP) by carboxylesterases. 4-piperidino-piperidine-carboxylate spontaneously hydrolyzes to 4PP and CO[2] after step 2. b, Structure-based sequence alignments of rabbit CE (rCE), human CE 1 (hCE1) and human intestinal CE (hiCE) obtained with ClustalW40 and refined using the rCE structure. Conserved residues are in black and nonconserved residues in magenta. Dotted lines indicate missing residues in the rCE structure. N-linked glycosylation sequences, disulfide bonds and putative gate residues are framed in black, and members of the catalytic triad are marked with an asterisk. The catalytic domain is blue; the domain, green; and the regulatory domain, red. c, Structure of rabbit liver carboxylesterase indicating the three domains: catalytic, and regulatory. Coloring as in (b), with catalytic residues in green, N-linked glycosyl groups in cyan and disulfide linkages in orange. d, The active site of rCE (green) superimposed on that of two esterases closely related in structure: triacylglycerol hydrolase (PDB entry 1THG; gold) and cholesterol esterase (2BCE; magenta). The catalytic Glu 353 of rCE is rotated away from the active site relative to orientations observed in other esterases. Glu 353 and His 467 lie adjacent to regions of structural disorder in rCE. e, Stereo view of a composite simulated-annealing omit map (cyan; contoured at 1.0 ) and the final [A]-weighted^34 2F[o] - F[c] map (magenta; contoured at 1.0 ) around the Asn 79 glycosylation site (both maps at 2.5 resolution).
Figure 3.
Figure 3. Structural basis of CPT-11 activation by rCE. a, Stereo view of the gate between the active site (green) and bound 4PP molecule (purple). The regulatory domain (red) is composed of helices 9, 10, 11 and 14, and the gate residues are Leu 252, Ser 254, Ile 387 and Leu 424 (cyan). The residues that mark the beginning and end of the disordered regions of the structure (Phe 354, Lys 371, Glu 459 and His 467) are also labeled. b, A proposed mechanism for the activation of CPT-11 by rCE. CPT-11 (orange) enters from the top of the catalytic gorge and fits well into the active site (catalytic Ser 221 and Glu 353 in green). After cleavage, the alcohol product (SN-38; magenta) leaves via the catalytic gorge, while the acyl product (4PP; purple) moves past the gate residues (cyan) and docks adjacent to the regulatory domain (red) on the surface of the molecule.
Figures reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 337-342) copyright 2002.
PDB entries for which this is a key reference: 1k4y.
L.Zhang, W.Liu, J.Xiao, T.Hu, J.Chen, K.Chen, H.Jiang, X.Shen. (2007). Malonyl-CoA: acyl carrier protein transacylase from Helicobacter pylori: Crystal structure and its interaction with acyl carrier protein. Protein Sci, 16, 1184-1192. [PubMed id: 17525466]
Figure 2.
Figure 2. (A) The topology diagram of HpMCAT. (Cylinders) Helices; (arrows) strands. The alignment was produced by the topology cartoon server from
Figure 4.
Figure 4. H-bond network around the active site. Atoms are shown as
Figures reprinted by permission from the Protein Society: Protein Sci (2007, 16, 1184-1192) copyright 2007.
PDB entries for which this is a key reference: 2h1y.