How to get 2d/3d structural coordinates from a PDB file?

Question

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

Answer 1

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.