Calculation of Antibody Fab Fragment
by B. Rupp, A. Zemla and R. Stanfield
The purpose of this program is to
allow consistent and convenient calculation of antibody Fab fragment elbow angles. The elbow
angle is used as a measure for relative displacement of the variable (V) and
constant domains (C) upon antigen binding. Please read the following to understand the workings and limitations of the
Calculation of elbow angles
Limitations and accuracy
Please cite the published reference when you
use this program:
Mandatory: a Fab fragment structure in valid
PDB format. Only ATOM records of the light and heavy chain will be read. Kabat numbering of residues optimal but not necessary.
Chain IDs. Any alphanumeric character, will
be converted to uppercase. The preset default ChainID of the chains is L and H. Take
care not to swap L <> H chains - the program cannot recognize this error.
Residue Number of Domain boundaries.
Integer. The beginning and end residue number of the VL, VH, CL and CH domains.
Preset defaults that work well with Kabat numbering are set. If there are less
residues than you specify, only the residues actually found in the PDB file will be used.
a form containing diagnostics, statistics, and a file list.
Diagnostics. The input file is processed and
split into the light and heavy chains defined by ChainID and the four domains VL,
VH, CL, and CH. Actually found residue numbers, domain boundaries, and atom
The domains are automatically aligned and superimposed (mobile VL onto static VH,
mobile CL onto static CH, both V domains on 1BBD, and the rotation of both C
domains of the V-aligned Fab onto 1BBD C) using the LGA program. The superposition
statistics (domain alignment, rmsd, transformation matrix) are checked for plausibility.
The key steps of the calculation and its validation are reported. Euler angles,
Euler vectors, and the pseudo-dyade angle between the two Euler axes are listed. Complement ambiguity is
resolved by checking the rotation angle of the C-domains relative to 1BBD (used
as standard 127 deg) following the method by Stanfield and Wilson. Unexpected
deviations from pseudo-2fold rotation or swapped L/H chain assignments are checked and warnings issued. Please
see CAVEATS. And of course, no guarantees and responsibility for anything
A list superimposed coordinate files of the domains of available for download is
First enter your email address in the box below.
Be sure that your email address is correct.
Your data will be processed and the result of RBOW analysis sent automatically
to the above address.
Bear in mind that if you enter an incorrect email address there is no way the
server can contact you!
Enter Fab PDB file name and options
File to upload in PDB format :
Chain ID for Light Chain
and Heavy Chain