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CATH-summer-2018 / SFAM-naming

Repository for materials that are related to superfamily naming
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General chopping issues #2

Open ilsenatorov opened 6 years ago

ilsenatorov commented 6 years ago

3wajA Seems badly chopped - boundary between domains 2 and 3 is in the middle of a beta-sheet and domains 2 is missing beta sheets that should be in.

ilsenatorov commented 6 years ago

4m0wA According to the article the protein has 4 domains, so domain 4m0wA03 needs to be split in 2, they are called palm and fingers in the article

ilsenatorov commented 6 years ago

4a15A Borders between domain A01 and A02 need to be moved by a couple of aminoacids according to the article. In the article domain is called "FeS cluster domain"

ilsenatorov commented 6 years ago

3hj6A/B Strange chopping, also forms superfamily 3.40.1620.20. Accroding to the article it should be a whole domain.

andrabujan commented 6 years ago

3cuz A01/02 According to the article, superfamily 1.20.1220.12 should be called 'malate synthase domain III' (residues 414–533) but superfamily 3.20.20.360 already has this name and it actually refers to domains I and II.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2578798/

andrabujan commented 6 years ago

1zhxA (superfamilies 1.20.120.1290 and 2.40.160.120, A03/A04) Article suggests chopping in smaller domains. [https://www.sciencedirect.com/science/article/pii/S0039128X13001372?via%3Dihub] - see figure 2 and annotations.

1.20.120.1290 contains CC domain and a part of ORD domain (badly chopped?) 2.40.160.120 contains the LD domain and most of ORD. Also PH, DD and FFAT domains need to be assigned a superfamily - A01/A02)

andrabujan commented 6 years ago

2w02 (! in the paper it says 2wO2, not 0, although 0 is correct - checked)

Superfamilies 1.10.340.60, 1.10.150.640, 3.10.450.440 (+ other unassigned) - need rechopping; According to paper - Domain 1 (residues 7 - 147, “thumb”), Domain 2 (residues 381 - 587, “palm”), Domain 3 (residues 198 - 380, fingers).

currently in CATH -> thumb domain = 1.10.340.60 + 3.10.450.440 (different chopping) finger domain = unassigned palm domain = 1.10.150.640 (different chopping)

link to the article -> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644304/

andrabujan commented 6 years ago

2w8m

needs to be split in 2 - catalytic domain and DNA recognition domain, according to the paper doi: 10.1128/JVI.01663-09 see comment in superfamily 3.40.1350.50.

andrabujan commented 6 years ago

3e2d

In the paper, the inserts from the crown domain have different residues than the structures represented in superfamilies 3.30.40.70 and 1.10.1200.140 (both have the same PDB 3e2d). According to the paper - Insert II (residues 325–351), Insert III (residues 361–394), Insert IV (residues 405–450) https://doi.org/10.1016/j.bbapap.2008.09.020.