How to unify all the subunits in a PDB file?
If you don't care about residue and atom numbering, which you probably do, then sed '/^TER/d' &lt; 1A3N.pdb &gt; 1A3N_combined.pdb will do. Since atom entries must be reordered, it looks like MDAnalysis will strip the TER entries automatically:

#!/usr/bin/env python2

import MDAnalysis


u = MDAnalysis.Universe('1A3N.pdb')

with MDAnalysis.Writer('1A3N_combined.pdb') as writer:
    writer.write(u)


So,

ATOM   1067  NH1 ARG A 141      26.176   8.362  17.810  1.00 11.11           N
ATOM   1068  NH2 ARG A 141      24.650   9.068  16.200  1.00 13.86           N
ATOM   1069  OXT ARG A 141      26.697  14.784  20.720  1.00 10.99           O
TER    1070      ARG A 141
ATOM   1071  N   HIS B   2       3.670 -13.643  19.447  1.00 38.58           N
ATOM   1072  CA  HIS B   2       2.695 -14.734  19.744  1.00 32.83           C
ATOM   1073  C   HIS B   2       1.379 -14.140  20.199  1.00 30.79           C


becomes

ATOM   1067  NH1 ARG A 141      26.176   8.362  17.810  1.00 11.11      A    N
ATOM   1068  NH2 ARG A 141      24.650   9.068  16.200  1.00 13.86      A    N
ATOM   1069  OXT ARG A 141      26.697  14.784  20.720  1.00 10.99      A    O
ATOM   1070  N   HIS B   2       3.670 -13.643  19.447  1.00 38.58      B    N
ATOM   1071  CA  HIS B   2       2.695 -14.734  19.744  1.00 32.83      B    C
ATOM   1072  C   HIS B   2       1.379 -14.140  20.199  1.00 30.79      B    C


where there are now chain IDs in the last column. See how this doesn't renumber residues? Modify the script; resids is a property, so the in-place object mutation works properly:

#!/usr/bin/env python2

import numpy as np
import MDAnalysis


u = MDAnalysis.Universe('1A3N.pdb')
u.residues.resids = np.arange(1, 1 + len(u.residues.resids))

with MDAnalysis.Writer('1A3N_combined.pdb') as writer:
    writer.write(u)


Finally:

ATOM   1067  NH1 ARG A 141      26.176   8.362  17.810  1.00 11.11      A    N
ATOM   1068  NH2 ARG A 141      24.650   9.068  16.200  1.00 13.86      A    N
ATOM   1069  OXT ARG A 141      26.697  14.784  20.720  1.00 10.99      A    O
ATOM   1070  N   HIS B 142       3.670 -13.643  19.447  1.00 38.58      B    N
ATOM   1071  CA  HIS B 142       2.695 -14.734  19.744  1.00 32.83      B    C
ATOM   1072  C   HIS B 142       1.379 -14.140  20.199  1.00 30.79      B    C