8GZ4 | pdb_00008gz4

Crystal structure of MPXV phosphatase

• PDB DOI: https://doi.org/10.2210/pdb8GZ4/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Monkeypox virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-25 Released: 2023-05-17 
• Deposition Author(s): Yang, H.T., Wang, W., Huang, H.J., Ji, X.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of monkeypox H1 phosphatase, an antiviral drug target.

Cui, W., Huang, H., Duan, Y., Luo, Z., Wang, H., Zhang, T., Nguyen, H.C., Shen, W., Su, D., Li, X., Ji, X., Yang, H., Wang, W.

(2023) Protein Cell 14: 469-472

• PubMed: 37285262 
• DOI: https://doi.org/10.1093/procel/pwac051
• Primary Citation Related Structures: 
  8GZ4

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Organizational Affiliation: 
• Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610064, China.
State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing 210023, China.
Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300450, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.85 kDa 
• Atom Count: 1,489 
• Modeled Residue Count: 170 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase H1	A	171	Monkeypox virus	Mutation(s): 0  Gene Names:  H1L, MPXV-CAM1990_02-083, MPXV-Congo_8-084, MPXV-COP-085, MPXV-GAB1988_001-084, MPXV-Ikubi-083, MPXV-M2940_FCT-089, MPXV-M2957_Lagos-089, MPXV-M3021_Delta-089, MPXV-M5312_HM12_Rivers-089, MPXV-M5320_M15_Bayelsa-082, MPXV-Nig_SEV71_2_82-084, MPXV-PCH-086, MPXV-Singapore-089, MPXV-SL-085, MPXV-UK_P1-089, MPXV-UK_P2-089, MPXV-UK_P3-089, MPXV-USA2003_099_GR-089, MPXV-USA2003_206_DM-089, MPXV-USA2003_223_RS-089, MPXV-UTC-080, MPXV-W_Nigeria-084, MPXV-WRAIR085, MPXV297957_080, MPXV298464_071, MPXV_DRC_Yandongi_092, MPXV_LIB1970_184_096, MPXV_RCG2003_358_096, MPXV_ROC_2010_035, MPXV_SUD2005_01_092, MPXV_USA2003_039_096, MPXV_USA2003_044_096, MPXV_ZAI1979_005_096, MPXVgp091, PDLMKLCO_00094 EC: 3.1.3 (PDB Primary Data), 3.1.3.48 (UniProt)
UniProt
Find proteins for A0A7H0DN78 (Monkeypox virus) Explore A0A7H0DN78  Go to UniProtKB:  A0A7H0DN78

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.48	α = 90
b = 62.48	β = 90
c = 170.494	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Yang, H.T., Wang, W., Huang, H.J., Ji, X.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81902063

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Refinement description
• Version 1.2: 2023-12-06
  Changes: Database references