3
$\begingroup$

I encountered the dichotomy in the context of PDBx/mmcif files, say, 6OSQ: each chain has a _entity_poly.pdbx_seq_one_letter_code but also _entity_poly.pdbx_seq_one_letter_code_can which i assume stands for "canonical". The raw and the canonical sequences.

The difference seems to be that all the ligands, hetatoms and other junk ((PSU), (MP4), (MG4)) have been removed from the the raw sequence to make it canonical i.e. it can now be packaged as fasta.

My question is where does one find documentation for this process? Is making it amenable to fasta tools the primary motivation? What kind of hetero atoms can occur there? Where is the logic written down for replacing them or deleting them when deriving the canonical sequence? Is the job of the structure's depositor or the PDB? Is there a tool for this?

Below is chain 1 of PDB6OSQ. First is the raw seq, then is the canonical one.

1 polyribonucleotide no yes
;GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG
GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA
AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA
UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG
AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGC
GUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC
UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAU(1MG)(PSU)(5MU)GAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCA
AUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACU
GUUUCGGCAAGGGGGUCAACCCGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACAC
GGCGGG(PSU)GCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUG
GGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCAC
UGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUU
GGGUAGGGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUA
AGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGU
CGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGG
GGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAA
AUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAU
CAGGUAACAUCAAAUCGUACCCCAAACCGACAC(6MZ)GGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGG
GUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAU
ACGGUGUGACGCCU(2MG)CCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCG
GUAAACGGCGGCCG(PSU)AAC(3TD)A(PSU)AACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGA
C(5MC)UGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUG(6MZ)AG
AUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGU(G7M)AACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGA
UGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUU
UGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCC
UAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUU
GACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUC
AACGGAUAAAAGGUACUCCG(2MG)GGAUAACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGC
A(OMC)CUCG(2MA)(PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGC(OMU)GUUCGCCA
UUUAAAGUGGUACGCGAGC(PSU)GGGUUUAGAACGUCGUGAGACAGU(PSU)CGGUCCCUAUCUGCCGUGGGCGCUGGA
GAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCAC
UGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGA
CCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUA
ACCGGUACUAAUGAACCGUGAGGCUUAACCU
;
;GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG
GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA
AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA
UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG
AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGC
GUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC
UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGA
GAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGG
GGGUCAACCCGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAA
GGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUG
CGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCGG
GUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAG
GCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGU
GAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUC
GUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGAAAUCAGUCGAAGAUAC
CAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGG
UGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACC
CGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUA
UAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGU
AGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGU
UAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUC
GACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCA
UUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGU
AGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAA
GGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU
$\endgroup$

2 Answers 2

2
$\begingroup$

You can check specification of pdbx_seq_one_letter_code and pdbx_seq_one_letter_code_can. These items are generated from the depositor-provided sequence on the PDB side. I suppose that the software used is MAXIT.

Note: these are not PDB files. They are distributed by the PDB organization, but the file format is mmCIF (or, more formally, PDBx/mmCIF).

$\endgroup$
1
  • $\begingroup$ Thanks Marcin, love the gemmi package. You are right, i was talking about mmcif imprecisely. I did find those references, but they seem a little incomplete at least.. For example they don't describe this (PSU) element which i found in literally the first mmcif file on my computer that i opened. I know now that (PSU) is pseudo-uracil because i stumbled across some .txt doc file, but i can't find it anymore. $\endgroup$
    – rtviii
    Jan 27, 2023 at 20:47
2
$\begingroup$

So, i was little myopic when reading the PDB description the first few times, but roughly what i was looking for is this:

  1. the non-canonical sequence(pdbx_seq_one_letter_code) makes explicit the ligands present in the given chain.
  2. the full dictionary of these is called the CCD and contains ~20000 entries, is curated and updated weekly by the PDB. That's basically their database (glorified text file over ftp) against which they check whether a given ligand has already been recorded.
  3. the process of chaffing them out of the EM dough as well as schema and more context canbe found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243272/pdf/bau116.pdf
$\endgroup$
1
  • 1
    $\begingroup$ ... the non-canonical sequence(pdbx_seq_one_letter_code) makes explicit the ligands present in the given chain.... now you have to explain how ligands are assigned to relevant chain A instead of equally close one chain BB ? $\endgroup$
    – pippo1980
    Jan 29, 2023 at 12:56

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.