Microbial 'omics


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protein-structure-txt [artifact]

Table of Contents

TXT

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

🔙 To the main page of anvi’o programs and artifacts.

Provided by

anvi-export-structures

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

This is a Protein Data Bank (X.pdb) file that describes the structure of a protein as stored in your structure-db. This is the output of running anvi-export-structures.

This file format has its own Wikipedia page, as well as pages on PDB-101 for beginners and for coordinates specifically, but is also briefly explained here.

The header describes the title (if one exists), the type of data (denoted by EXPDTA), and any free-form annotations (denoted by REMARK ). In Anvi’o, these are primarily MODELLER information calculated when you ran anvi-gen-structure-database.

Most of the data will describe the position of individual atoms (denoted by ATOM) in your protein, where columns 6, 7, and 8 describe the three dimensional coordinate of the atom. The rest of the columns describe information like what position that atom is in the amno acid.

TER statements separate independent chains from each other.

Here is an example:

EXPDTA    THEORETICAL MODEL, MODELLER 9.22 2020/10/13 14:38:54
REMARK   6 MODELLER OBJECTIVE FUNCTION:       255.0071
REMARK   6 MODELLER BEST TEMPLATE percent SEQ ID:  73.077
ATOM      1  N   MET A   1       4.009  -3.600  -0.411  1.00 59.26           N
ATOM      2  CA  MET A   1       5.250  -3.864  -1.173  1.00 59.26           C
ATOM      3  CB  MET A   1       6.409  -3.005  -0.631  1.00 59.26           C
ATOM      4  CG  MET A   1       6.204  -1.504  -0.854  1.00 59.26           C
ATOM      5  SD  MET A   1       7.545  -0.444  -0.229  1.00 59.26           S
ATOM      6  CE  MET A   1       6.982  -0.449   1.495  1.00 59.26           C
ATOM      7  C   MET A   1       5.617  -5.306  -1.058  1.00 59.26           C
ATOM      8  O   MET A   1       4.900  -6.175  -1.552  1.00 59.26           O
ATOM      9  N   SER A   2       6.753  -5.603  -0.397  1.00 49.70           N
ATOM     10  CA  SER A   2       7.165  -6.971  -0.290  1.00 49.70           C
ATOM     11  CB  SER A   2       8.547  -7.150   0.362  1.00 49.70           C
ATOM     12  OG  SER A   2       9.546  -6.534  -0.437  1.00 49.70           O
ATOM     13  C   SER A   2       6.184  -7.694   0.556  1.00 49.70           C
ATOM     14  O   SER A   2       5.954  -7.346   1.714  1.00 49.70           O
ATOM     15  N   GLU A   3       5.553  -8.718  -0.037  1.00103.21           N
ATOM     16  CA  GLU A   3       4.632  -9.540   0.676  1.00103.21           C
ATOM     17  CB  GLU A   3       3.856 -10.490  -0.249  1.00103.21           C
ATOM     18  CG  GLU A   3       4.774 -11.467  -0.988  1.00103.21           C
ATOM     19  CD  GLU A   3       3.918 -12.407  -1.826  1.00103.21           C
ATOM     20  OE1 GLU A   3       2.672 -12.402  -1.638  1.00103.21           O
ATOM     21  OE2 GLU A   3       4.502 -13.146  -2.663  1.00103.21           O
ATOM     22  C   GLU A   3       5.402 -10.410   1.614  1.00103.21           C
...
ATOM    594  C   ASN A  79      19.969 -15.504   4.267  1.00 61.57           C
ATOM    595  O   ASN A  79      21.042 -14.862   4.423  1.00 61.57           O
ATOM    596  OXT ASN A  79      19.857 -16.742   4.474  1.00 61.57           O
TER     597      ASN A  79
END

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