6Y8H | pdb_00006y8h

Novel p38-alpha crystal lattice with highly exposed p38/TAB1 non-canonical PPI surface.

• PDB DOI: https://doi.org/10.2210/pdb6Y8H/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-03-05 Released: 2020-03-11 
• Deposition Author(s): De Nicola, G.F., Nichols, C.E.
• Funding Organization(s): British Heart Foundation, Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Novel p38-alpha crystal lattice with highly exposed p38/TAB1 non-canonical PPI surface.

De Nicola, G.F., Nichols, C.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.93 kDa 
• Atom Count: 3,105 
• Modeled Residue Count: 344 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Mus musculus	Mutation(s): 1  Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811  Go to UniProtKB:  P47811

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SB4	B [auth A]	4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE C18 H19 F N6 VSPFURGQAYMVAN-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
SB4	BindingDB:  6Y8H	IC50: min: 19, max: 20 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.864	α = 90
b = 102.325	β = 90
c = 103.821	γ = 90

Software Package:

Software Name	Purpose
DIALS	data collection
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): De Nicola, G.F., Nichols, C.E.

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Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	SP/14/2/30922, FS/14/29/30896
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_PC_17164

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description