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PDBsum entry 1hap
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Hydrolase/hydrolase inhibitor/DNA
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PDB id
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1hap
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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An ambiguous structure of a DNA 15-Mer thrombin complex.
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Authors
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K.Padmanabhan,
A.Tulinsky.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1996,
52,
272-282.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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The structure of a complex between thrombin and a GGTTGGTGTGGTTGG DNA 15-mer has
been analyzed crystallographically. The solution NMR structure of the 15-mer has
two stacked G-quartets similar to that found in the previous X-ray structure
determination of the 15-mer-thrombin complex [Padmanabhan, Padmanabhan, Ferrara,
Sadler & Tulinsky (1993). J. Biol. Chem. 268, 17651-17654]; the strand
polarity, however, is reversed from that of the crystallographic structure. The
structure of the complex here has been redetermined with better diffraction data
confirming the previous crystallographic structure but also indicating that the
NMR solution structure fits equally well. Both 15-mer complex structures refined
to an R value of about 0.16 presenting a disconcerting ambiguity. Since the two
15-mer structures associate with thrombin in different ways (through the TGT
loop in the X-ray and TT loop in the NMR model), other independent lines of
physical or chemical evidence are required to resolve the ambiguity.
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Figure 1.
Fig. 1. Schematic drawings of the X-ray (left) and NMR (right)
structures of the aptamer. "IT loops span wide grooves, TGT spans
narrow groove in X-ray structure and
vice versa
in NMR structure.
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Figure 7.
Fig. 7. Stereoview of the hydrophobic
interaction sites of T3 and TI2 of
the NMR model of the aptamer.
The DNA is shown in thin lines
and thrombin residues, which form
the hydrophobic pockets located in
the fibrinogen exosite at top (in
bold). Heparin binding-site inter-
actions at bottom (primed resi-
dues). Only bases with good
density shown.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1996,
52,
272-282)
copyright 1996.
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Secondary reference #1
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Title
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The structure of alpha-Thrombin inhibited by a 15-Mer single-Stranded DNA aptamer.
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Authors
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K.Padmanabhan,
K.P.Padmanabhan,
J.D.Ferrara,
J.E.Sadler,
A.Tulinsky.
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Ref.
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J Biol Chem, 1993,
268,
17651-17654.
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PubMed id
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