9WWF | pdb_00009wwf

Crystal structure of human tyrosylprotein sulfotransferase 2 (TPST2) in Mn2+-bound state

• PDB DOI: https://doi.org/10.2210/pdb9WWF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-23 Released: 2025-12-31 
• Deposition Author(s): Jin, M., Yang, J., Kim, H., Eom, S.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human tyrosylprotein sulfotransferase 2 (TPST2) in Mn2+-bound state

Jin, M., Yang, J., Kim, H., Eom, S.H.

To be published.

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: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 36.73 kDa 
• Atom Count: 2,686 
• Modeled Residue Count: 303 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine sulfotransferase 2	A	322	Homo sapiens	Mutation(s): 0  Gene Names: TPST2 EC: 2.8.2.20
UniProt & NIH Common Fund Data Resources
Find proteins for O60704 (Homo sapiens) Explore O60704  Go to UniProtKB:  O60704
PHAROS:  O60704 GTEx:  ENSG00000128294

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	E [auth A]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	B [auth A], C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.817	α = 90
b = 102.817	β = 90
c = 103.115	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Jin, M., Yang, J., Kim, H., Eom, S.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C1006267
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2024-00344154
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2024-00440614

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release