Search

Text Color

Margin Size

Font Type

Enable Dyslexic Font

iCn3D Intro Tutorial A: Modeling a Short Peptide in a Protein

Last updated

Jan 9, 2025
Save as PDF
- iCn3D Basics: Saving Files
- iCn3D Intro Tutorial B: Rendering a Protein

$\newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}}$

$\newcommand{\id}{\mathrm{id}}$ $\newcommand{\Span}{\mathrm{span}}$

( \newcommand{\kernel}{\mathrm{null}\,}\) $\newcommand{\range}{\mathrm{range}\,}$

$\newcommand{\RealPart}{\mathrm{Re}}$ $\newcommand{\ImaginaryPart}{\mathrm{Im}}$

$\newcommand{\Argument}{\mathrm{Arg}}$ $\newcommand{\norm}[1]{\| #1 \|}$

$\newcommand{\inner}[2]{\langle #1, #2 \rangle}$

$\newcommand{\Span}{\mathrm{span}}$

$\newcommand{\id}{\mathrm{id}}$

$\newcommand{\Span}{\mathrm{span}}$

$\newcommand{\kernel}{\mathrm{null}\,}$

$\newcommand{\range}{\mathrm{range}\,}$

$\newcommand{\RealPart}{\mathrm{Re}}$

$\newcommand{\ImaginaryPart}{\mathrm{Im}}$

$\newcommand{\Argument}{\mathrm{Arg}}$

$\newcommand{\norm}[1]{\| #1 \|}$

$\newcommand{\inner}[2]{\langle #1, #2 \rangle}$

$\newcommand{\Span}{\mathrm{span}}$ $\newcommand{\AA}{\unicode[.8,0]{x212B}}$

$\newcommand{\vectorA}[1]{\vec{#1}} % arrow$

$\newcommand{\vectorAt}[1]{\vec{\text{#1}}} % arrow$

$\newcommand{\vectorB}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vectorC}[1]{\textbf{#1}}$

$\newcommand{\vectorD}[1]{\overrightarrow{#1}}$

$\newcommand{\vectorDt}[1]{\overrightarrow{\text{#1}}}$

$\newcommand{\vectE}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash{\mathbf {#1}}}}$

$\newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}}$

$\newcommand{\avec}{\mathbf a}$

$\newcommand{\bvec}{\mathbf b}$

$\newcommand{\cvec}{\mathbf c}$

$\newcommand{\dvec}{\mathbf d}$

$\newcommand{\dtil}{\widetilde{\mathbf d}}$

$\newcommand{\evec}{\mathbf e}$

$\newcommand{\fvec}{\mathbf f}$

$\newcommand{\nvec}{\mathbf n}$

$\newcommand{\pvec}{\mathbf p}$

$\newcommand{\qvec}{\mathbf q}$

$\newcommand{\svec}{\mathbf s}$

$\newcommand{\tvec}{\mathbf t}$

$\newcommand{\uvec}{\mathbf u}$

$\newcommand{\vvec}{\mathbf v}$

$\newcommand{\wvec}{\mathbf w}$

$\newcommand{\xvec}{\mathbf x}$

$\newcommand{\yvec}{\mathbf y}$

$\newcommand{\zvec}{\mathbf z}$

$\newcommand{\rvec}{\mathbf r}$

$\newcommand{\mvec}{\mathbf m}$

$\newcommand{\zerovec}{\mathbf 0}$

$\newcommand{\onevec}{\mathbf 1}$

$\newcommand{\real}{\mathbb R}$

$\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}$

$\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}$

$\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}$

$\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}$

$\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}$

$\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}$

$\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}$

$\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}$

$\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}$

$\newcommand{\laspan}[1]{\text{Span}\{#1\}}$

$\newcommand{\bcal}{\cal B}$

$\newcommand{\ccal}{\cal C}$

$\newcommand{\scal}{\cal S}$

$\newcommand{\wcal}{\cal W}$

$\newcommand{\ecal}{\cal E}$

$\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}$

$\newcommand{\gray}[1]{\color{gray}{#1}}$

$\newcommand{\lgray}[1]{\color{lightgray}{#1}}$

$\newcommand{\rank}{\operatorname{rank}}$

$\newcommand{\row}{\text{Row}}$

$\newcommand{\col}{\text{Col}}$

$\renewcommand{\row}{\text{Row}}$

$\newcommand{\nul}{\text{Nul}}$

$\newcommand{\var}{\text{Var}}$

$\newcommand{\corr}{\text{corr}}$

$\newcommand{\len}[1]{\left|#1\right|}$

$\newcommand{\bbar}{\overline{\bvec}}$

$\newcommand{\bhat}{\widehat{\bvec}}$

$\newcommand{\bperp}{\bvec^\perp}$

$\newcommand{\xhat}{\widehat{\xvec}}$

$\newcommand{\vhat}{\widehat{\vvec}}$

$\newcommand{\uhat}{\widehat{\uvec}}$

$\newcommand{\what}{\widehat{\wvec}}$

$\newcommand{\Sighat}{\widehat{\Sigma}}$

$\newcommand{\lt}{<}$

$\newcommand{\gt}{>}$

$\newcommand{\amp}{&}$

$\definecolor{fillinmathshade}{gray}{0.9}$

A. Modeling short sections of a protein chain

Pick one of the small protein fragments below for modeling using iCn3D

PDB	Description of protein (all small fragments)
2YW8	Crystal structure of human RUN and FYVE domain-containing protein
6EEY	human Scribble PDZ4 R1110G Mutant
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
6L1C	PHF20L1 Tudor1 Y24L mutant
3D2N	MBNL1 tandem zinc finger 1 and 2 domain
3RD2	NIP45 SUMO-like Domain 2
7NZC	SH3 domain of POSH (Plenty of SH3 Domains protein)
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
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
3I8Z	human chromobox homolog 4 (CBX4)
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

Color	Paste snip of renderings as shown below.
Spectrum, Selection to better see each amino acids in selection
Charge Gray if no charges (ignore yellow highlight)
Hydrophobicity (if nonpolar like oil)
Atom (red oxygen, blue nitrogen, yellow Sulfur

Support Center

How can we help?