Exercises in protein structure

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Exercises in protein structure
1. In beta-galactosidase (1dpo) has four
identical subunits (chains A, B, C, D). How many
atoms from each subunit are involved
(distancelt7Å) in each interface? (i.e. A B 42
atoms)
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2. In dihydrofolate reductase (7dfr) the mutant
S63Y has no activity, although it binds the
substrate, dihydrofolate. Why?
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3. In pancreatic ribonuclease (1onc), which
residues hydrogen-bond to the sulfate? Which
waters?
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4. In phytase (1ihp), how many crystallographic
waters are there? How any protein atoms are
making hydrogen bonds with at least one
crystallographic water? How many crystallographic
waters are not making H-bonds to the protein?
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5. Draw a TOPS diagram of the agglutinin (1jpc).
Find the CATH class and architecture for this
protein using only the structure (i.e. not the
name).
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6. Where are the sequence ranges for the two
domains of lysozyme (1L17)?
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7. In lysozyme (1L17), what do you predict will
happen if L121 is mutated to an arginine? What
about R96--gtL?
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8. In Anfinsens famous experiment, he raised
antibodies against fragments of pancreatic
ribonuclease (1ONC). Fragment 46-76 and fragment
62-85 were tried. Which fragments is most likely
to induce antibodies against the intact enzyme?
Why?
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9. Using PROCHECK (validation), find out how many
non-glycine residues have backbone angle phi gt 0
in beta-lactamase (1A7T), chain A.
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10. Using XRayView, determine the maximum
xtal-to-film distance allowed if the resolution
limit is 3.0Å.
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11. Using XRayView, determine the maximum
rotation angle for data collection on unknown5.