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PDBsum entry 1f8z
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Lipid binding protein
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PDB id
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1f8z
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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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Three-Dimensional nmr structure of the sixth ligand-Binding module of the human ldl receptor: comparison of two adjacent modules with different ligand binding specificities.
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Authors
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D.Clayton,
I.M.Brereton,
P.A.Kroon,
R.Smith.
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Ref.
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FEBS Lett, 2000,
479,
118-122.
[DOI no: ]
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PubMed id
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Abstract
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The sixth ligand-binding module of the low-density lipoprotein receptor
contributes to the binding of apolipoprotein B100-containing lipoproteins. 1H
NMR spectroscopy, DYANA and X-PLOR structure calculations were used to determine
that this module has a well defined structure with a backbone conformation
similar to other modules. Structures from calculations that simulated the
presence of a calcium ion showed increased resolution without large increases in
energy, increased deviations from idealised geometry or violations of
experimental constraints. Investigation of the surface properties of this module
indicates there are significant differences from the fifth module, which binds
apolipoprotein E-containing lipoproteins in addition to apolipoprotein
B100-containing lipoproteins.
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Figure 2.
Fig. 2. The 20 lowest energy structures of LB6 calculated
in (a) the absence of constraints for the calcium ion and (b)
the presence of distance constraints for the four conserved
acidic residues corresponding to those identified to be
equatorial Ca^2+ ligands in LB5. c: Shows secondary structural
elements identified in structures shown in (b).
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Figure 4.
Fig. 4. Primary sequence and distribution of surface charge
and hydrophobicity in LB5 and LB6 (lowest energy structure).
Residues shown in bold are common to both modules; residues
marked with filled squares are coordinated to calcium in LB5;
and those underlined are unique (across all modules) to LB5
between the first and last cysteine residue. Modules in a and d
have an similar orientation to that of Fig. 2, then are shown
(left to right) rotated in two anticlockwise 90° steps, as
viewed from the bottom, around the vertical axis. Positively
charged functional groups are shown in blue, negatively charged
groups are shown in red, and the sidechains of large non-polar
residues (F, I, L, M, V, W) are shown in green.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS Lett
(2000,
479,
118-122)
copyright 2000.
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