The 2nd half of heavy and light chains cannot align with the original chain, does it suggest some issues with the trauncation process?
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5. special case: 4hjj_1P
[4HJJ](https://www.rcsb.org/structure/4HJJ) is a **Dual Variable Domain** Immunoglobulin (DVD-Ig)
pdb4hjj_1P.cho variable domain CDR is not interacting with the antigen.
In the original PDB file of 4HJJ, based on its structure, **H126-H246** and **L114-L224** looks like the second variable domain and is interacting with the antigen, is the correct variable domain to trauncate.
.cho
files.cho
files not found: see below for a list of identifiers.cho
files that where neither Heavy nor Light chains are present.cho
file where Length SEQRES < ATMSEQ:e.g. pdb1dee_2.cho alignment with original chain
pdb1dee_2.cho chain H
vs. original1dee chain F
pdb1dee_2.cho_H QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYY 1dee_F QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYY
pdb1dee_2.cho_H ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVS 1dee_F ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVS
pdb1dee_2.cho_H QVQLVES------GGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYD 1dee_F SGSASAPTLFPLVSCENSNPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVL . . . :..:: :. .. .. : : .. . .:
pdb1dee_2.cho_H ESNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQG 1dee_F RGGKYAATS--------------QVLLPSKDVAQGTNEHVVCKV-Q--H---PNGNKEKD ... : :.: . : . . :.
pdb1dee_2.cho_H TLVTVS 1dee_F VPL--- . :
CLUSTAL O(1.2.3) multiple sequence alignment
pdb1dee_2.cho_L DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS 1dee_E DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
pdb1dee_2.cho_L RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTDIQMTQ---SP 1dee_E RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTVAAPSVFIFPP ***** : *
pdb1dee_2.cho_L SSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSG 1dee_E SDEQLKSG-TASVVCL-------LNNFYPREAK----VQWKVDNALQSGNSQESVTEQDS . . . .::. :* :: : . .:**** .. . ..
pdb1dee_2.cho_L T------DFTLTISSLQPEDFATYYCQQSY---SA--PRTFGQGTKVEIKRT 1dee_E KDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC------ . . **:. : .. . : :: : ::.: