7NRY

Re-refinement of MAPKAP kinase-2/inhibitor complex 3fyj

7NRY の概要

• エントリーDOI: 10.2210/pdb7nry/pdb
• 分子名称: MAP kinase-activated protein kinase 2, (10R)-10-methyl-3-(6-methylpyridin-3-yl)-9,10,11,12-tetrahydro-8H-[1,4]diazepino[5',6':4,5]thieno[3,2-f]quinolin-8-one, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: mk-2, mk2, mapkap-2, ser/thr kinase, map kinase, alternative splicing, atp-binding, kinase, nucleotide-binding, phosphoprotein, polymorphism, serine/threonine-protein kinase, transferase
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38411.72

構造登録者

Croll, T.I.,Read, R.J. (登録日: 2021-03-04, 公開日: 2022-02-09, 最終更新日: 2024-01-31)

主引用文献

Croll, T.I.,Read, R.J.
Adaptive Cartesian and torsional restraints for interactive model rebuilding.
Acta Crystallogr D Struct Biol, 77:438-446, 2021

PubMed Abstract: When building atomic models into weak and/or low-resolution density, a common strategy is to restrain their conformation to that of a higher resolution model of the same or similar sequence. When doing so, it is important to avoid over-restraining to the reference model in the face of disagreement with the experimental data. The most common strategy for this is the use of `top-out' potentials. These act like simple harmonic restraints within a defined range, but gradually weaken when the deviation between the model and reference grows beyond that range. In each current implementation the rate at which the potential flattens at large deviations follows a fixed form, although the form chosen varies among implementations. A restraint potential with a tuneable rate of flattening would provide greater flexibility to encode the confidence in any given restraint. Here, two new such potentials are described: a Cartesian distance restraint derived from a recent generalization of common loss functions and a periodic torsion restraint based on a renormalization of the von Mises distribution. Further, their implementation as user-adjustable/switchable restraints in ISOLDE is described and their use in some real-world examples is demonstrated.

PubMed: 33825704
DOI: 10.1107/S2059798321001145

実験手法

X-RAY DIFFRACTION (3.8 Å)