7NRB

Re-refinement of MK3-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3fhr


Literature

Adaptive Cartesian and torsional restraints for interactive model rebuilding.

Croll, T.I.Read, R.J.

(2021) Acta Crystallogr D Struct Biol 77: 438-446

  • DOI: https://doi.org/10.1107/S2059798321001145
  • Primary Citation of Related Structures:  
    7NRB, 7NRY

  • 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.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, Keith Peters Building, Cambridge CB2 0XY, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 3336Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK3
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16644 (Homo sapiens)
Explore Q16644 
Go to UniProtKB:  Q16644
PHAROS:  Q16644
GTEx:  ENSG00000114738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16644
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4O
Query on P4O

Download Ideal Coordinates CCD File 
B [auth A]2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE
C21 H16 N4 O
OWFLADWRSCINST-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.688α = 90
b = 74.832β = 107.34
c = 60.664γ = 90
Software Package:
Software NamePurpose
ISOLDErefinement
PHENIXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom209407/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description