8YPF | pdb_00008ypf

The crystal structure of inactive p38 complexed with a ATF2 from 46 to 90

PDB DOI: https://doi.org/10.2210/pdb8YPF/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-16 Released: 2025-03-19
Deposition Author(s): Zhang, Y.Y., Pei, C.J., He, Q.Q., Luo, Z.P., Wu, J.W., Wang, Z.X.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.218 (Depositor), 0.218 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Structural and mechanistic insights into the allosteric activation of p38alpha MAP kinase via specific docking interactions

Zhang, Y.Y., Pei, C.J., He, Q.Q., Luo, Z.P., Wu, J.W., Wang, Z.X.

To be published.

Macromolecule Content

Total Structure Weight: 46.42 kDa
Atom Count: 2,991
Modeled Residue Count: 343
Deposited Residue Count: 405
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Mus musculus	Mutation(s): 0 Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811 Go to UniProtKB: P47811
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47811
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic AMP-dependent transcription factor ATF-2	B	45	Homo sapiens	Mutation(s): 0 Gene Names: ATF2, CREB2, CREBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P15336 (Homo sapiens) Explore P15336 Go to UniProtKB: P15336
PHAROS: P15336 GTEx: ENSG00000115966
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15336
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218 (Depositor), 0.218 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.873	α = 90
b = 81.873	β = 90
c = 122.585	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0802500
Ministry of Science and Technology (MoST, China)	China	2022YFA0806504

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.