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PDBsum entry 1krn
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Serine protease
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PDB id
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1krn
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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 human plasminogen kringle 4 at 1.68 a and 277 k. A possible structural role of disordered residues.
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Authors
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B.Stec,
A.Yamano,
M.Whitlow,
M.M.Teeter.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1997,
53,
169-178.
[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
percentage match of
84%.
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Abstract
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Despite considerable effort to elucidate the functional role of the kringle
domains, relatively little is known about interactions with other protein
domains. Most of the crystal structures describe the interactions at the kringle
active site. This study suggests a novel way to interpret structural results
such as disorder located away from an active site. The crystal structure of
human plasminogen kringle 4 (PGK4) has been refined against 10-1.68 A resolution
X-ray data (R(merge) = 3.7%) to the standard crystallographic R = 14.7% using
the program X-PLOR. The crystals of PGK4 showed significant instability in cell
dimensions (changes more than 1.5 A) even at 277 K. The refinement revealed
structural details not observed before [Mulichak, Tulinsky & Ravichandran
(1991). Biochemistry, 30, 10576-10588], such as clear density for additional
side chains and more extensive disorder. Discrete disorder was detected for
residues S73, S78, T80, S89, S91, S92, Ml12, S132, C138 and K142. Most of the
disordered residues form two patches on the surface of the protein. This
localized disorder suggests that these residues may play a role in quaternary
interactions and possibly form an interface with the other domains of proteins
that contain kringles, such as plasminogen. Although, an additional residue D65
was refined at the beginning of the sequence, still more residues near the
peptide cleavage site must be disordered in the crystal.
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Figure 10.
Fig. 10. Bifurcated hydrogen
bond of His96NE2. Close
contacts are also provided
by carbonyl O atoms to
the carbon H atoms of the
imidazole ring. The
2Fo- Fc
electron density is contoured
at the 1.5cr level.
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Figure 11.
Fig. 11. Trifurcated hydrogen
bond of His98 (H98) NE2.
The hydrogen bond between
Met93 (M93) SD and the
carbonyl O atom is also
depicted, as are short contacts
to CE1.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1997,
53,
169-178)
copyright 1997.
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