9NYM | pdb_00009nym

Crystal structure of an MKP5 allosteric loop mutant, N448A

PDB DOI: https://doi.org/10.2210/pdb9NYM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-27 Released: 2025-07-30
Deposition Author(s): Manjula, R., Bennett, A.M., Lolis, E.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.241 (Depositor), 0.247 (DCC)
R-Value Work:
0.194 (Depositor), 0.195 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of an MKP5 allosteric loop mutant, N448A

Manjula, R., Bennett, A.M., Lolis, E.

To be published.

Macromolecule Content

Total Structure Weight: 34.24 kDa
Atom Count: 2,453
Modeled Residue Count: 294
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase 10	A, B	148	Homo sapiens	Mutation(s): 0 Gene Names: DUSP10, MKP5 EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6W6 (Homo sapiens) Explore Q9Y6W6 Go to UniProtKB: Q9Y6W6
PHAROS: Q9Y6W6 GTEx: ENSG00000143507
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6W6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.241 (Depositor), 0.247 (DCC)
R-Value Work: 0.194 (Depositor), 0.195 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.31	α = 74.62
b = 40.531	β = 78.86
c = 57.38	γ = 61.55

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	RO1 HL158876

Revision History (Full details and data files)

Version 1.0: 2025-07-30
Type: Initial release

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.