7XYD

Crystal structure of TMPRSS2 in complex with Nafamostat

• PDB DOI: https://doi.org/10.2210/pdb7XYD/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2022-06-01 Released: 2023-12-06 
• Deposition Author(s): Wang, H., Liu, X., Duan, Y., Liu, X., Sun, L., Yang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.248 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Crystal structure of TMPRSS2 in complex with Nafamostat

Wang, H., Duan, Y., Liu, X., Sun, L., Yang, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 88.7 kDa 
• Atom Count: 5,833 
• Modelled Residue Count: 735 
• Deposited Residue Count: 790 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2 catalytic chain	A, C [auth B]	146	Homo sapiens	Mutation(s): 5  Gene Names: TMPRSS2, PRSS10
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393  Go to UniProtKB:  O15393
PHAROS:  O15393 GTEx:  ENSG00000184012

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2 catalytic chain	B [auth C], D	249	Homo sapiens	Mutation(s): 0  Gene Names: TMPRSS2, PRSS10
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393  Go to UniProtKB:  O15393
PHAROS:  O15393 GTEx:  ENSG00000184012

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GBS (Subject of Investigation/LOI)	G [auth C], J [auth D]	4-carbamimidamidobenzoic acid C8 H9 N3 O2 SXTSBZBQQRIYCU-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	F [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.248 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.14	α = 90
b = 93.203	β = 100.6
c = 93.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Wang, H., Liu, X., Duan, Y., Liu, X., Sun, L., Yang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92169109

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release