9CHY | pdb_00009chy

Crystal structure of the human MESH1 (D66K)-PAPS complex

PDB DOI: https://doi.org/10.2210/pdb9CHY/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-07-02 Released: 2025-12-10
Deposition Author(s): Rose, J., Zhou, P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.221 (Depositor), 0.221 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.174 (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

MESH1 Functions as a Metazoan PAPS Phosphatase to Regulate Sulfation.

Lin, C.-C., Rose, J., Zhang, A., Mirando, A.J., Mestre, A.A., Ding, C.C., Liao, Y., Chen, S.-Y., Setayeshpour, Y., Wu, J., Li, Z., Yan, D., Hilton, M.J., Zhou, P., Chi, J.-T.

(2025) Nat Chem Biol

Macromolecule Content

Total Structure Weight: 42.3 kDa
Atom Count: 3,223
Modeled Residue Count: 359
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1	A, B	180	Homo sapiens	Mutation(s): 1 Gene Names: HDDC3, MESH1 EC: 3.1.7.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4P3 (Homo sapiens) Explore Q8N4P3 Go to UniProtKB: Q8N4P3
PHAROS: Q8N4P3 GTEx: ENSG00000184508
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N4P3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PPS (Subject of Investigation/LOI) Query on PPS Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE C₁₀ H₁₅ N₅ O₁₃ P₂ S GACDQMDRPRGCTN-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]