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iCn3D Intro Tutorial B: Rendering a Protein

Last updated

Jan 9, 2025
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- iCn3D Intro Tutorial A: Modeling a Short Peptide in a Protein
- iCn3D Intro Tutorial C: Finding Pockets in Proteins

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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)

1HDO	Human biliverdin IX beta reductase: NADP complex
2HC2	Engineered protein tyrosine phosphatase beta catalytic domain
5ZUN	Crystal structure of human monoacylglycerol lipase in complex with compound 3l
1X3S	Crystal structure of human Rab18 in complex with Gppnhp
4IN0	Crystal Structure of human splicing factor dim2/TXNL4B
1KGD	Crystal Structure of the Guanylate Kinase-like Domain of Human CASK
5KQL	Co-crystal structure of LMW-PTP in complex with 2-oxo-1-phenyl-2-(phenylamino)ethanesulfonic acid
1QGV	HUMAN SPLICEOSOMAL PROTEIN U5-15KD
1MF7	INTEGRIN ALPHA M I DOMAIN
4RQR	Crystal Structure of Human Glutaredoxin with MESNA
4JKA	Open and closed forms of R1865A human PRP8 RNase H-like domain with bound Co ion
5C4M	RhoA GDP with novel switch II conformation
6P0J	Crystal structure of GDP-bound human RalA
4MMM	Human Pdrx5 complex with a ligand BP7
4M6IJ	Crystal structure of human dihydrofolate reductase (DHFR) bound to NADPH
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.

Results (replace image with yours)

PDB ID, description:

ribbon
Cylinder and plate
C alpha trace
backbone
line
sphere

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.

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