swiss-pdbviewer introduction-wenwen wang
TRANSCRIPT
SPDBV
PDB
Tools
Selection
Labeling
Display
Measuring
Mutation
Torsions
Coloring
Protein & Component
Structural Alignment
Homology Modeling
1. Download and Install
• Downloading the PDB files in your own PC
PDB home page http://www.rcsb.org/pdb/home/home.do
• Downloading Swiss-PdbViewer
http://spdbv.vital-it.ch/download.html
Protein structure database: Protein data bank (PDB)
• The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography or NMR spectroscopy
• The PDB is a key resource in areas of structural biology.
http://www.pdb.org/pdb/home/home.do
Structure Entity Hits
29 entries available
PDB ID of this entry TK from virus
with ligand (substrate)
X-ray crystallography
Structure and related data (1KIM)
Related data on each tag
The citation of this entry
Visualization of biological assembly
Download and Install PdbViewer
• Download Swiss-PdbViewer
http://spdbv.vital-it.ch/download.html
• Download user guide
http://spdbv.vital-it.ch/Swiss-PdbViewerManualv3.7.pdf
• Tutorial video (English)
http://www.youtube.com/watch?v=nYT5qwtfNew&feature=related
http://www.youtube.com/watch?v=yFE3CAHNkZg
3. Control panel van der Waals dots spheres
C-white O-red N-blue S-yellow P-orange H-cyan Other-gray
4. Tools
Center
Enlarge
Translate Rotate
Distance between 2 atoms
Angle between 3 atoms
omega, phi and psi angles
Identify atoms
Display groups that are at a certain distance
from a selected atom
Center the molecule on one atom
Fit a molecule onto an other
Mutation
Torsion
4.1 Measure distance between 2 atoms
---Open 1CRN ---Select ---Group Kind ---SS bonds ---Show only ---Side chain ---Label ---Measure the distance between 2 Cα of Cys which have disulphide bonds ---Pick 1st atom ---Pick 2nd atom ---Hit “Esc”
4.2 Measure Angle between 3 atoms
---Press button ---pick center atom ---pick 2nd atom ---pick 3rd atom ---Esc
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4.3 Measure of omega, phi and psi angles of the picked amino-acid
---Press “Ctrl” key + button ---pick 4 atoms ---measure the torsion angle of any specific bond ---Esc 1
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4.6 Torsions
---Open---1KIM ---select THM1 ---only show THM1 ---label it ---color it orange ---Zoom in & Center ---render in solid 3D ---select one atom and display groups at 6A ---Show & Center ---col---white ---THM1 orange ---Tool ---Compute H-Bonds ---Display ---Show H-Bonds Distance ---only select THM1 ---Show Only H-Bonds from Selection ---Select ---Pick on Screen ---Gln125 & Tyr101 ---color them blue ---Torsion ---pick one atom ---pick 2nd atom
5.3 Color in Residue Type acting on Ribbon
Type: Gray-non polar amino acid: Val, Leu, Pro, Ala, Trp, Gly, Met, Phe, Cys, Ile Yellow-polar amino acid: Ser, Thr, Asn, Try, Gln Red-negtive charge (acid amino acid): Asp, Glu Blue-positive charge (basic amino acid): Lys, His, Arg
6.1 Enzyme-ligand interaction---Merging
---Loading PDB file of protease ---Color---Chain ---Loading PDB file of inhibitor ---Merging 2 layers ---Alignment window---select protease---Select---All ---select inhibitor ---Edit---Create Merged Layer from Selection (by layer)
6.2 Enzyme-ligand interaction---Active site
---display only groups that are within 10A of the center atom of inhibitor ---Center the molecule ---label them ---Tools ---Compute H-Bonds
6.2 Enzyme-ligand interaction---Active site
---select I121145 in Control Panel ---Display ---Show Only H-Bonds from Selection
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6.2 Enzyme-ligand interaction---Active site
---remove the other labels, only label residues interact with inhibitor, and color them pink ---Display ---Show H-Bonds Distances
7.1 Structural Alignment-Magic Fit
---Loading sars.pdb ---Loading IBV.pdb ---Color---Layer ---click the reset-view button ---Wind ---Alignment ---Fit ---Iterative Magic ---aligned residues are shaded in gray ---show structures in ribbon
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8.1 Homology Modeling: register with Swiss-Model
http://swissmodel.expasy.org/workspace/index.php?func=account_create1
>Murine_HV SGIVKMVSPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCRVTSSDFCVMSGRMSLTVMSYQMQGCQLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNGRPQGAFHVTLRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGNFYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAIFNRCNWFVQSDSCSLEEFNVWAMTNGFSSIKADLVLDALASMTGVTVEQVLAAIKRLHSGFQGKQILGSCVLEDELTPSDVYQQLAGVKLQ
8.3 Loading Raw Sequence
8.4 Load template structure
---loading raw amino acid sequence: Murine_HV.fasta ---loading SARS protease with known 3D structure: 2h2zA.pdb
2h2zA
Murine_HV