iCn3D Intro Tutorial A: Modeling a Short Peptide in a Protein
- Page ID
- 114282
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)A. Modeling short sections of a protein chain
Pick one of the small protein fragments below for modeling using iCn3D
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PDB |
Description of protein (all small fragments) |
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2YW8 |
Crystal structure of human RUN and FYVE domain-containing protein |
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6EEY |
human Scribble PDZ4 R1110G Mutant |
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2PA1 |
PDZ domain of human PDLIM2 bound to a C-terminal extension from human beta-tropomyosin |
|
3A03 |
Hox11L1 homeodomain |
|
3IWL |
cisplatin bound to a human copper chaperone (monomer) |
|
5Z2S |
DUX4-HD2 domain |
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6L1C |
PHF20L1 Tudor1 Y24L mutant |
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3D2N |
MBNL1 tandem zinc finger 1 and 2 domain |
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3RD2 |
NIP45 SUMO-like Domain 2 |
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7NZC |
SH3 domain of POSH (Plenty of SH3 Domains protein) |
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1I2T |
HUMAN HYPERPLASTIC DISCS PROTEIN: AN ORTHOLOG OF THE C-TERMINAL DOMAIN OF POLY(A)-BINDING PROTEIN |
|
1NTE |
CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENI |
|
2Y9U |
Structural basis of p63a SAM domain mutants involved in AEC syndrome |
|
2FMA |
Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in 'small unit cell' form, atomic resolution |
|
4OU0 |
Crystal Structure of RPA32C |
|
1ZT3 |
C-terminal domain of Insulin-like Growth Factor Binding Protein-1 isolated from human amniotic fluid |
|
2E3H |
Crystal structure of the CLIP-170 CAP-Gly domain 2 |
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1L9L |
GRANULYSIN FROM HUMAN CYTOLYTIC T LYMPHOCYTES |
|
5EFM |
Beclin 1 Flexible-helical Domian (FHD) (141-171) |
|
2BZX |
Atomic model of CrkL-SH3C monomer |
|
1NHL |
SNAP-23N Structure |
|
7UW7 |
Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ADP |
|
4N7F |
3rd WW domain of human Nedd4-1 |
|
2Q9V |
C890S mutant of the 4th PDZ domain of human membrane-associated guanylate kinase |
|
6T9Q |
second, C-terminal repeat of the DNA-binding domain of human TImeless |
|
1WVN |
domain 3 of human alpha polyC binding protein |
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3I8Z |
human chromobox homolog 4 (CBX4) |
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2F60 |
Dihydrolipoamide Dehydrogenase (E3)-Binding Domain of Human E3-Binding Protein |
|
7FGN |
FAF1 UBL1 |
|
5UM3 |
V122L mutant of human UBR-box domain from UBR2 |
|
2FJZ |
Alzheimer's Amyloid Precursor Protein (APP) copper-binding domain (residues 133 to 189) in 'small unit cell' form, metal-free |
1. Open https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
2. Input in your assigned pdb code and select Load Biological Unit
3. Choose Analysis, Seq and Annotation
4. Choose Details tab and uncheck conserved domains
5. With your mouse, select, hold, and sweep between the first 5-10 amino acids (given in single letter code) as illustrated below. When you select them, they will turn yellow.
6. Choose View, View Selection (to limit view to what you want
7. Choose Style, Proteins, Sticks to see all the bonds
8. Change the background from black by choosing from top menu bar Style, Background, Transparent
9. Choose, Analysis, Label, Per residue/#; then Analysis, Label Scale, 2
10. Next, color your model as shown below in different ways as described in the table below. Then take a screen capture of the selection and replace the image in the table cell with your own
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Color |
Paste snip of renderings as shown below. |
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Spectrum, Selection |
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Charge (ignore yellow highlight) |
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Hydrophobicity (if nonpolar like oil) |
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Atom (red oxygen, blue nitrogen, yellow Sulfur |
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