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MCL-1 is not capped at C terminus? #75

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IAlibay opened this issue Oct 11, 2022 · 3 comments
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MCL-1 is not capped at C terminus? #75

IAlibay opened this issue Oct 11, 2022 · 3 comments
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@bobym
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Release 0.3.0

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@IAlibay
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IAlibay commented Oct 11, 2022

Linked to #68, MCL-1 does not have a cap at the C terminus even though 4HW3 states that the protein is missing residues 322 and 323.

Is this intentional?
@IAlibay
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IAlibay commented Oct 11, 2022

pinging @bobym

@IAlibay IAlibay added this to the Release 0.3.0 milestone Oct 11, 2022
@bobym bobym self-assigned this Oct 11, 2022
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bobym commented Oct 11, 2022

Looking back at my notes, this stems from a misunderstanding of the assay protocol. The authors assayed the ligands using an MCL1 construct that had the last 5 AA deleted. I misread the residues in the 4WH3 structure and thought the missing residues were a part of that deletion because the numbering in their SI and the PDB are different. Opening a PR to fix this now.

@bobym bobym linked a pull request Oct 11, 2022 that will close this issue
[WIP] Fix MCL1 capping, curate thrombin ligands for expanded dynamic range #76
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@IAlibay IAlibay mentioned this issue Oct 24, 2022
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bobym added a commit that referenced this issue Oct 24, 2022
@bobym
Update protein.pdb
2f2eae2 
Replace MCL1 protein.pdb for issue #75
IAlibay added a commit that referenced this issue Dec 6, 2022
@bobym @IAlibay
Addressing issues 75 & 81 (#82)
e9b153e 
* Addressing issues 75 & 81

1. Updating MCL1 protein.pdb to have caps.

2. Replacing all ligands.sdf with new versions to fix the ligand distortions seen in issue #81

3. Adding re-curated thrombin ligands (expanded ligand set)

* Update protein.pdb

Replace MCL1 protein.pdb for issue #75

* Remove extra pfkfb3 ligands.yaml entry

* add missing lig_43 yaml entry for mcl1

* Add missing lig_49220392 pde2 ligands.yaml entry

* Add missing lig_CHEMBL3265000 from syk ligands.yaml file

* Add missing lig_3, lig_E28, lig_E5, lig_11 from shp2 ligands.yaml

* Fix thrombin ligands.yaml file

* Add POP to pfkfb3 cofactors, remove from protein pdb

* Disable unused html comparisons

* Add codecov token

Co-authored-by: IAlibay <[email protected]>
@ijpulidos
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This has been solved via #82

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@ijpulidos @IAlibay @bobym