Working with protein structures. Benjamin Jack

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Transcription:

Working with protein structures Benjamin Jack

Structure of Triosephosphate Isomerase PDB ID: 1HTI loop beta sheet alpha helix

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Structure of Basic Fibroblast Growth Factor PDB ID: 1BFG beta sheet

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PDB files can contain multiple chains Chain A (blue) human TfR1 Chain B (green) Machupo virus GP1 PDB ID: 3KAS

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Anatomy of a PDB file HEADER GROWTH FACTOR 15-APR-93 1BFG TITLE CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC FIBROBLAST GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS GROWTH FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.KITAGAWA,H.AGO,Y.KATSUBE,A.FUJISHIMA,Y.MATSUURA REVDAT 3 24-FEB-09 1BFG 1 VERSN REVDAT 2 01-APR-03 1BFG 1 JRNL REVDAT 1 31-JAN-94 1BFG 0 JRNL AUTH H.AGO,Y.KITAGAWA,A.FUJISHIMA,Y.MATSUURA,Y.KATSUBE JRNL TITL CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH JRNL TITL 2 FACTOR AT 1.6 A RESOLUTION. JRNL REF J.BIOCHEM.(TOKYO) V. 110 360 1991 JRNL REFN ISSN 0021-924X JRNL PMID 1769963

Anatomy of a PDB file HEADER GROWTH FACTOR 15-APR-93 1BFG TITLE CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC FIBROBLAST GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS GROWTH FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.KITAGAWA,H.AGO,Y.KATSUBE,A.FUJISHIMA,Y.MATSUURA REVDAT 3 24-FEB-09 1BFG 1 VERSN REVDAT 2 01-APR-03 1BFG 1 JRNL REVDAT 1 31-JAN-94 1BFG 0 JRNL AUTH H.AGO,Y.KITAGAWA,A.FUJISHIMA,Y.MATSUURA,Y.KATSUBE JRNL TITL CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH JRNL TITL 2 FACTOR AT 1.6 A RESOLUTION. JRNL REF J.BIOCHEM.(TOKYO) V. 110 360 1991 JRNL REFN ISSN 0021-924X JRNL PMID 1769963

Anatomy of a PDB file HEADER GROWTH FACTOR 15-APR-93 1BFG TITLE CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC FIBROBLAST GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS GROWTH FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.KITAGAWA,H.AGO,Y.KATSUBE,A.FUJISHIMA,Y.MATSUURA REVDAT 3 24-FEB-09 1BFG 1 VERSN REVDAT 2 01-APR-03 1BFG 1 JRNL REVDAT 1 31-JAN-94 1BFG 0 JRNL AUTH H.AGO,Y.KITAGAWA,A.FUJISHIMA,Y.MATSUURA,Y.KATSUBE JRNL TITL CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH JRNL TITL 2 FACTOR AT 1.6 A RESOLUTION. JRNL REF J.BIOCHEM.(TOKYO) V. 110 360 1991 JRNL REFN ISSN 0021-924X JRNL PMID 1769963

Anatomy of a PDB file HEADER GROWTH FACTOR 15-APR-93 1BFG TITLE CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC FIBROBLAST GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS GROWTH FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.KITAGAWA,H.AGO,Y.KATSUBE,A.FUJISHIMA,Y.MATSUURA REVDAT 3 24-FEB-09 1BFG 1 VERSN REVDAT 2 01-APR-03 1BFG 1 JRNL REVDAT 1 31-JAN-94 1BFG 0 JRNL AUTH H.AGO,Y.KITAGAWA,A.FUJISHIMA,Y.MATSUURA,Y.KATSUBE JRNL TITL CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH JRNL TITL 2 FACTOR AT 1.6 A RESOLUTION. JRNL REF J.BIOCHEM.(TOKYO) V. 110 360 1991 JRNL REFN ISSN 0021-924X JRNL PMID 1769963

Anatomy of a PDB file ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file atom number ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file atom name ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file residue name ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file chain ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file residue number ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file x, y, z coordinates ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file occupancy ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

Anatomy of a PDB file B factor ATOM 1 N ASP A 19 6.864 13.397-2.220 1.00 40.02 N ATOM 2 CA ASP A 19 6.806 14.455-1.186 1.00 38.62 C ATOM 3 C ASP A 19 7.688 14.002-0.016 1.00 36.01 C ATOM 4 O ASP A 19 8.837 14.477 0.052 1.00 35.96 O ATOM 5 CB ASP A 19 5.372 14.834-0.851 1.00 43.28 C ATOM 6 CG ASP A 19 5.264 16.239-0.268 1.00 46.36 C ATOM 7 OD1 ASP A 19 5.447 16.322 0.978 1.00 48.00 O ATOM 8 OD2 ASP A 19 5.015 17.239-0.970 1.00 48.45 O ATOM 9 N PRO A 20 7.165 13.125 0.822 1.00 33.63 N ATOM 10 CA PRO A 20 7.888 12.572 1.982 1.00 30.69 C ATOM 11 C PRO A 20 9.049 11.697 1.528 1.00 27.78 C

command line/ console object control panel viewer mouse controls

Object Control Panel A (Actions): Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations S (Show): Change the way things appear, e.g. change to stick or cartoon view. H (Hide): Things that are shown using S accumulate, and don't automatically replace the last view. H is the opposite of S and hides unwanted representations. L (Label): Label atoms, residues, etc. C (Color): Change the color of atoms and groups.

PyMOL exercises 1. Download & open structure 3KAS: fetch 3KAS Display in various forms (cartoon, stick, spheres, ) Color different chains Zoom in to display protein-protein interface 2. Download & open structure 1DLW Display as cartoon Show heme as sticks Make a ray-traced image using the Ray button

Anything you can do with a menu, you can do with a command fetch 1DHF - download a PDB file select chain A - selects chain A select 1DHF - selects whole structure (http://pymol.sourceforge.net/newman/user/s0220commands.html) hide everything - hides everything show ribbon - shows current selection as ribbon show_as ribbon, chain A - shows chain A as ribbon

Every command has a python counterpart PyMOL: select chain A Python: cmd.select( chain A ) Need help? (PyMOL command line) help select

Putting it all together: Running python scripts in PyMOL my_script.py: cmd.fetch( 12AS ) PyMOL command line: run my_script.py

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