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PDBsum entry 2v7n
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Immune system
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PDB id
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2v7n
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References listed in PDB file
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Key reference
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Title
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Structure of the recombinant antibody FAB fragment f3p4.
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Authors
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D.Frey,
T.Huber,
A.Plückthun,
M.G.Grütter.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2008,
64,
636-643.
[DOI no: ]
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PubMed id
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Abstract
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The structure of the antibody Fab fragment f3p4, which was selected from a
subset of the synthetic HuCAL antibody library to bind the sodium citrate
symporter CitS, is described at 1.92 A resolution. Comparison with computational
models revealed deviations in a few framework positions and in the binding
loops. The crystals belong to space group P2(1)2(1)2 and contain four molecules
in the asymmetric unit, with unit-cell parameters a=102.77, b=185.92, c=102.97
A. These particular unit-cell parameters allowed pseudo-merohedral twinning;
interestingly, the twinning law relates a twofold screw axis to a twofold axis.
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Figure 5.
Figure 5 Structure of CDR-L3. A superposition of the main-chain
atoms (for clarity, carbonyl O atoms are omitted from the
figure) of CDR-L3 of the Fab fragment f3p4 (grey) with typical
members of the V[  ]and
V[  ]families
is shown. In V[ ]members
CDR-L3 adopts a hairpin-like structure (magenta; PDB code 8fab
). In V[ ]members,
which predominantly have a proline at position L136 (Kabat L95),
the CDR-L3 has an  -loop
conformation (yellow; PDB code 1ay1 ). The conformation of the
CDR-L3 of Fab fragment f3p4 is an intermediate conformation, but
is also present in naturally occurring antibodies with a proline
residue at L136 (Kabat L95; green; PDB code 1c1e ). The compared
molecules have an equal number of residues in CDR-L3 and all C^
 atoms
of L106-L140 (Kabat L88-99) were used for the superposition.
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Figure 7.
Figure 7 Surface representation of the binding region. C^ traces
of CDR-H1, CDR-H2, CDR-H3, CDR-L1, CDR-L2 and CDR-L3 are shown
and coloured red, green, blue, cyan, magenta and yellow,
respectively. Residues Arg H108 (Kabat H94) and Asp H137 (Kabat
H101) forming the conserved hydrogen bonds as well as the
solvent-exposed residue Tyr L40 (Kabat L32) are shown in stick
representation.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2008,
64,
636-643)
copyright 2008.
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