iCn3D Intro Tutorial B: Rendering a Protein
- Page ID
- 114283
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)B. Rendering Full Proteins
Pick one of the proteins below that has both alpha helices and beta sheets. You will then change the protein style (rendering) to see the same protein in different ways to illustrate different properties of the proteins.
Monomeric proteins with alpha (helices) and beta (sheets)
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1HDO |
Human biliverdin IX beta reductase: NADP complex |
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2HC2
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Engineered protein tyrosine phosphatase beta catalytic domain |
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5ZUN |
Crystal structure of human monoacylglycerol lipase in complex with compound 3l |
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1X3S |
Crystal structure of human Rab18 in complex with Gppnhp |
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4IN0 |
Crystal Structure of human splicing factor dim2/TXNL4B |
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1KGD |
Crystal Structure of the Guanylate Kinase-like Domain of Human CASK |
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5KQL |
Co-crystal structure of LMW-PTP in complex with 2-oxo-1-phenyl-2-(phenylamino)ethanesulfonic acid |
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1QGV |
HUMAN SPLICEOSOMAL PROTEIN U5-15KD |
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1MF7 |
INTEGRIN ALPHA M I DOMAIN |
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4RQR |
Crystal Structure of Human Glutaredoxin with MESNA |
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4JKA |
Open and closed forms of R1865A human PRP8 RNase H-like domain with bound Co ion |
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5C4M |
RhoA GDP with novel switch II conformation |
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6P0J |
Crystal structure of GDP-bound human RalA |
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4MMM |
Human Pdrx5 complex with a ligand BP7 |
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4M6IJ |
Crystal structure of human dihydrofolate reductase (DHFR) bound to NADPH |
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3M9J |
Crystal structure of human thioredoxin C69/73S double mutant, reduced form |
1. Load ID 4LPK, Crystal Structure of K-Ras protein with a small molecule, GDP, bound
2. Choose Color, Secondary, Sheet in Yellow
3. Style, Background, White
4. Choose Style, Proteins and display as ribbon, cylinder and plate, C alpha trace, backbone, lines and sphere
5. Paste your results in the table below.
6.
Results (replace image with yours)
PDB ID, description:
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ribbon |
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Cylinder and plate |
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C alpha trace |
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backbone |
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line |
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sphere |
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7. Model a protein dimer that has two subunits. Use the pdb code for 1LFD (CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS). Paste your favorite image below.
8. Model a huge structure, the human rhinovirus 14 (causes colds, PDB: 4RHV). It so big you have to load it in a different way, as shown below. Paste your favorite image below.
