8YGW | pdb_00008ygw

The Crystal Structure of MAPK11 from Biortus

PDB DOI: https://doi.org/10.2210/pdb8YGW/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-27 Released: 2024-03-13
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Lin, D., Guo, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.278 (Depositor), 0.284 (DCC)
R-Value Work:
0.205 (Depositor), 0.211 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The Crystal Structure of MAPK11 from Biortus.

Wang, F., Cheng, W., Yuan, Z., Lin, D., Guo, S.

To be published.

Macromolecule Content

Total Structure Weight: 41.93 kDa
Atom Count: 2,697
Modeled Residue Count: 326
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 11	A	364	Homo sapiens	Mutation(s): 0 Gene Names: MAPK11, PRKM11, SAPK2, SAPK2B EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q15759 (Homo sapiens) Explore Q15759 Go to UniProtKB: Q15759
PHAROS: Q15759 GTEx: ENSG00000185386
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B96 (Subject of Investigation/LOI) Query on B96 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA C₃₁ H₃₇ N₅ O₃ MVCOAUNKQVWQHZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.278 (Depositor), 0.284 (DCC)
R-Value Work: 0.205 (Depositor), 0.211 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.061	α = 90
b = 61.86	β = 90
c = 147.437	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-03-13
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.