Partial Walkthrough of "Assignment" 1
This will give you a partial walkthrough (written by a student) of how to go about completing assignment 1.
Please be sure to attend next week's session for a more thorough and complete explanation!
Search and download PDB file
Start by going into RCSB Protein Data Bank's website.
Type in the PDB ID of the biomolecule you want and search.
Here you will find a lot of information about the biomolecule. You should look around and see what types of information are available. You can find the PDB text file to download on the left side.
You may also download the PDB text file directly from here or simply view it from your browser here.
Making sense of the PDB file
The first few lines contain header information about the biomolecule such as its name, author, literature references, etc.
HEADER TRANSFERASE(PHOSPHOTRANSFERASE) 08-JAN-93 1ATP
TITLE 2.2 ANGSTROM REFINED CRYSTAL STRUCTURE OF THE CATALYTIC
TITLE 2 SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE COMPLEXED WITH
TITLE 3 MNATP AND A PEPTIDE INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CAMP-DEPENDENT PROTEIN KINASE;
COMPND 3 CHAIN: E;
COMPND 4 EC: 2.7.1.37;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: PEPTIDE INHIBITOR PKI(5-24);
COMPND 8 CHAIN: I;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 MOL_ID: 2;
SOURCE 4 ORGANISM_SCIENTIFIC: MUS MUSCULUS
KEYWDS TRANSFERASE(PHOSPHOTRANSFERASE)
EXPDTA X-RAY DIFFRACTION
AUTHOR J.ZHENG,E.A.TRAFNY,D.R.KNIGHTON,N.-H.XUONG,S.S.TAYLOR,
AUTHOR 2 L.F.TENEYCK,J.M.SOWADSKI
REVDAT 1 15-APR-93 1ATP 0
JRNL AUTH J.ZHENG,E.A.TRAFNY,D.R.KNIGHTON,N.H.XUONG,
JRNL AUTH 2 S.S.TAYLOR,L.F.TEN EYCK,J.M.SOWADSKI
JRNL TITL 2.2 A REFINED CRYSTAL STRUCTURE OF THE CATALYTIC
JRNL TITL 2 SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE COMPLEXED
JRNL TITL 3 WITH MNATP AND A PEPTIDE INHIBITOR.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 49 362 1993
JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449
Next section is the remarks section, also meant to be read by humans. It gives lots of information about the experiment methods, techniques, results, etc.
The following section provides the amino acid sequences of each chain, beginning at the N-terminal. The third column indicates chain (in this example, we have two chains, E and I), fourth column indicates how many amino acids in that chain, and the following columns list the sequence of amino acids.
SEQRES 1 E 350 GLY ASN ALA ALA ALA ALA LYS LYS GLY SER GLU GLN GLU
SEQRES 2 E 350 SER VAL LYS GLU PHE LEU ALA LYS ALA LYS GLU ASP PHE
SEQRES 3 E 350 LEU LYS LYS TRP GLU THR PRO SER GLN ASN THR ALA GLN
SEQRES 4 E 350 LEU ASP GLN PHE ASP ARG ILE LYS THR LEU GLY THR GLY
SEQRES 5 E 350 SER PHE GLY ARG VAL MET LEU VAL LYS HIS LYS GLU SER
SEQRES 6 E 350 GLY ASN HIS TYR ALA MET LYS ILE LEU ASP LYS GLN LYS
SEQRES 7 E 350 VAL VAL LYS LEU LYS GLN ILE GLU HIS THR LEU ASN GLU
SEQRES 8 E 350 LYS ARG ILE LEU GLN ALA VAL ASN PHE PRO PHE LEU VAL
SEQRES 9 E 350 LYS LEU GLU PHE SER PHE LYS ASP ASN SER ASN LEU TYR
SEQRES 10 E 350 MET VAL MET GLU TYR VAL ALA GLY GLY GLU MET PHE SER
SEQRES 11 E 350 HIS LEU ARG ARG ILE GLY ARG PHE SER GLU PRO HIS ALA
SEQRES 12 E 350 ARG PHE TYR ALA ALA GLN ILE VAL LEU THR PHE GLU TYR
SEQRES 13 E 350 LEU HIS SER LEU ASP LEU ILE TYR ARG ASP LEU LYS PRO
SEQRES 14 E 350 GLU ASN LEU LEU ILE ASP GLN GLN GLY TYR ILE GLN VAL
SEQRES 15 E 350 THR ASP PHE GLY PHE ALA LYS ARG VAL LYS GLY ARG THR
SEQRES 16 E 350 TRP THR LEU CYS GLY THR PRO GLU TYR LEU ALA PRO GLU
SEQRES 17 E 350 ILE ILE LEU SER LYS GLY TYR ASN LYS ALA VAL ASP TRP
SEQRES 18 E 350 TRP ALA LEU GLY VAL LEU ILE TYR GLU MET ALA ALA GLY
SEQRES 19 E 350 TYR PRO PRO PHE PHE ALA ASP GLN PRO ILE GLN ILE TYR
SEQRES 20 E 350 GLU LYS ILE VAL SER GLY LYS VAL ARG PHE PRO SER HIS
SEQRES 21 E 350 PHE SER SER ASP LEU LYS ASP LEU LEU ARG ASN LEU LEU
SEQRES 22 E 350 GLN VAL ASP LEU THR LYS ARG PHE GLY ASN LEU LYS ASN
SEQRES 23 E 350 GLY VAL ASN ASP ILE LYS ASN HIS LYS TRP PHE ALA THR
SEQRES 24 E 350 THR ASP TRP ILE ALA ILE TYR GLN ARG LYS VAL GLU ALA
SEQRES 25 E 350 PRO PHE ILE PRO LYS PHE LYS GLY PRO GLY ASP THR SER
SEQRES 26 E 350 ASN PHE ASP ASP TYR GLU GLU GLU GLU ILE ARG VAL SER
SEQRES 27 E 350 ILE ASN GLU LYS CYS GLY LYS GLU PHE THR GLU PHE
SEQRES 1 I 20 THR THR TYR ALA ASP PHE ILE ALA SER GLY ARG THR GLY
SEQRES 2 I 20 ARG ARG ASN ALA ILE HIS ASP
Following sections provide information about HET groups, secondary structure elements, and crystal information.
Then comes the bulk of the pdb file, the ATOM records. Each line provides information about one atom, defined as shown below.
Atom Name XYZ coordinates
(CG = Carbon Gamma) Chain (in angstroms) Occupancy
\ / / | \ /
Atom# \ Amino Acid/ Amino Acid#/ | \ / B-factor
\ \ | / / / | \ / /
ATOM 146 CG GLU E 31 0.362 8.005 -23.998 1.00100.00 C
ATOM 147 CD GLU E 31 0.915 7.429 -25.259 1.00100.00 C
ATOM 148 OE1 GLU E 31 0.055 7.483 -26.258 1.00 96.20 O
ATOM 149 OE2 GLU E 31 2.038 6.951 -25.320 1.00 98.06 O
ATOM 150 N THR E 32 0.042 11.783 -21.629 1.00 95.23 N
ATOM 151 CA THR E 32 -0.349 13.144 -21.293 1.00 14.13 C
ATOM 152 C THR E 32 -0.291 13.360 -19.791 1.00 34.92 C
ATOM 153 O THR E 32 -1.285 13.365 -19.069 1.00 45.19 O
ATOM 154 CB THR E 32 -1.699 13.556 -21.967 1.00 43.93 C
ATOM 155 OG1 THR E 32 -2.131 12.551 -22.893 1.00 35.19 O
ATOM 156 CG2 THR E 32 -1.533 14.872 -22.729 1.00 18.94 C
ATOM 157 N PRO E 33 0.931 13.513 -19.326 1.00 41.99 N
ATOM 158 CA PRO E 33 1.203 13.723 -17.938 1.00 37.35 C
ATOM 159 C PRO E 33 0.718 15.099 -17.515 1.00100.00 C
ATOM 160 O PRO E 33 0.745 16.037 -18.334 1.00 21.69 O
ATOM 161 CB PRO E 33 2.735 13.669 -17.818 1.00 14.27 C
ATOM 162 CG PRO E 33 3.320 13.724 -19.217 1.00100.00 C
ATOM 163 CD PRO E 33 2.154 13.594 -20.175 1.00 19.71 C
ATOM 164 N SER E 34 0.275 15.204 -16.248 1.00 62.63 N
ATOM 165 CA SER E 34 -0.206 16.475 -15.725 1.00 17.64 C
ATOM 166 C SER E 34 0.911 17.336 -15.147 1.00 91.45 C
ATOM 167 O SER E 34 1.930 16.835 -14.654 1.00 35.12 O
Extra Credit: Using software to display the structure
Opening 1ATP.pdb with a viewer such as PyMOL can allow you to do fun things!
Here is what the surface of this molecule looks like. Note that green is carbon, oxygen is red, and nitrogen is blue.
Now let's show it with spheres:
Here's a cartoon diagram. The red structure on the bottom is the I chain (peptide inhibitor).
Let's model this with sticks now. Notice the orange in the middle.
Zooming in on that orange, can you tell what it is now? (hint: orange is phosphate)
Teal here represents the I chain. Zooming in on the last three amino acids, you can easily tell what they are (if you know your amino acids!)
Notice that this fits with the PDB file we read eariler:
SEQRES 1 I 20 THR THR TYR ALA ASP PHE ILE ALA SER GLY ARG THR GLY
SEQRES 2 I 20 ARG ARG ASN ALA ILE HIS ASP
Trivia: The background image on the homepage is of this structure!
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