<p>Molecular structures are 3D.
The records (lines) in the PDB files are in so-called fixed column format.<br />
The fields don't need to be separated with blank characters, but they must be in specified columns. For example, the X coordinate is in columns 31-38.
Here is the specification of the ATOM record from <a href="https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM" rel="nofollow noreferrer">PDB v3.3</a>.</p>
<pre><code>COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
 1 -  6        Record name   &quot;ATOM  &quot;
 7 - 11        Integer       serial       Atom  serial number.
13 - 16        Atom          name         Atom name.
17             Character     altLoc       Alternate location indicator.
18 - 20        Residue name  resName      Residue name.
22             Character     chainID      Chain identifier.
23 - 26        Integer       resSeq       Residue sequence number.
27             AChar         iCode        Code for insertion of residues.
31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
55 - 60        Real(6.2)     occupancy    Occupancy.
61 - 66        Real(6.2)     tempFactor   Temperature  factor.
77 - 78        LString(2)    element      Element symbol, right-justified.
79 - 80        LString(2)    charge       Charge  on the atom.
</code></pre>

CC BY-SA 4.0
2021-04-02T09:53:11.870Z
2021-04-02T09:53:11.870Z
marcin
<p>Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file.</p>
<p>I have looked a believe that the coordinates are in below line:</p>
<pre><code>ATOM   1067  NH1 ARG A 141     -10.147   7.455  -6.079  1.00 23.24           N  
</code></pre>
<p>but i am unable to make a sense from it as i don't know which one is (x/y/z) in (2d/3d) coordinate system.</p>
<p>If anyone describe it, that'll be a great help.</p>
<p>Thanks</p>

<proteins><protein-structure><pdb>
How to get 2d/3d structural coordinates from a PDB file?
# How to get 2d/3d structural coordinates from a PDB file?

(Asked by: username_0 on 2021-04-01)

Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file.
I have looked a believe that the coordinates are in below line:
ATOM   1067  NH1 ARG A 141     -10.147   7.455  -6.079  1.00 23.24           N  

but i am unable to make a sense from it as i don't know which one is (x/y/z) in (2d/3d) coordinate system.
If anyone describe it, that'll be a great help.
Thanks

**Tags:** proteins, protein-structure, pdb

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## 1 answers

### Answer by username_1 on 2021-04-02. Score: 3 | Accepted answer

Molecular structures are 3D.
The records (lines) in the PDB files are in so-called fixed column format.
The fields don't need to be separated with blank characters, but they must be in specified columns. For example, the X coordinate is in columns 31-38.
Here is the specification of the ATOM record from PDB v3.3.
COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
 1 -  6        Record name   "ATOM  "
 7 - 11        Integer       serial       Atom  serial number.
13 - 16        Atom          name         Atom name.
17             Character     altLoc       Alternate location indicator.
18 - 20        Residue name  resName      Residue name.
22             Character     chainID      Chain identifier.
23 - 26        Integer       resSeq       Residue sequence number.
27             AChar         iCode        Code for insertion of residues.
31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
55 - 60        Real(6.2)     occupancy    Occupancy.
61 - 66        Real(6.2)     tempFactor   Temperature  factor.
77 - 78        LString(2)    element      Element symbol, right-justified.
79 - 80        LString(2)    charge       Charge  on the atom.


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