3O8P | pdb_00003o8p

Conformational plasticity of p38 MAP kinase DFG motif mutants in response to inhibitor binding

• PDB DOI: https://doi.org/10.2210/pdb3O8P/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2010-08-03 Released: 2010-09-01 
• Deposition Author(s): Namboodiri, H.V., Karpusas, M., Bukhtiyarova, M., Springman, E.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.276 (Depositor) 
• R-Value Work: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Conformational plasticity of p38 MAP kinase DFG motif mutants in response to inhibitor binding

Namboodiri, H.V., Springman, E.B., Karpusas, M., Bukhtiyarova, M., Ramcharan, J.

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: 41.95 kDa 
• Atom Count: 3,030 
• Modeled Residue Count: 336 
• 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	Homo sapiens	Mutation(s): 1  Gene Names: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMU	B [auth A]	1-(5-TERT-BUTYL-2-METHYL-2H-PYRAZOL-3-YL)-3-(4-CHLORO-PHENYL)-UREA C15 H19 Cl N4 O FWIJKWMXNHRSRO-UHFFFAOYSA-N
BOG	C [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BMU	BindingDB:  3O8P	Kd: min: 1160, max: 1190 (nM) from 2 assay(s)
		IC50: min: 794, max: 2.10e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.276 (Depositor) 
• R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.931	α = 90
b = 73.587	β = 90
c = 76.828	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Namboodiri, H.V., Karpusas, M., Bukhtiyarova, M., Springman, E.B.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary