8V04

High resolution TMPRSS2 structure following acylation by nafamostat

• PDB DOI: https://doi.org/10.2210/pdb8V04/pdb

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


• Deposited: 2023-11-16 Released: 2024-01-31 
• Deposition Author(s): Fraser, B.J., Dong, A., Kutera, M., Seitova, A., Li, Y., Hutchinson, A., Edwards, A., Benard, F., Levon, H., Arrowsmith, C.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.181 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Starting Model: experimental

Literature

High resolution TMPRSS2 structure following acylation by nafamostat

Fraser, B.J., Dong, A., Kutera, M., Seitova, A., Li, Y., Hutchinson, A., Edwards, A., Benard, F., Levon, H., Arrowsmith, C.

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)

Macromolecule Content

• Total Structure Weight: 42.24 kDa 
• Atom Count: 3,228 
• Modelled Residue Count: 340 
• Deposited Residue Count: 359 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2 non-catalytic chain	A	110	Homo sapiens	Mutation(s): 5  Gene Names: TMPRSS2, PRSS10 EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393  Go to UniProtKB:  O15393
PHAROS:  O15393 GTEx:  ENSG00000184012
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: O15393-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	B	249	Homo sapiens	Mutation(s): 0  Gene Names: TMPRSS2 EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393  Go to UniProtKB:  O15393
PHAROS:  O15393 GTEx:  ENSG00000184012

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	N [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CIT	I [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GBS (Subject of Investigation/LOI)	H [auth B]	4-carbamimidamidobenzoic acid C8 H9 N3 O2 SXTSBZBQQRIYCU-UHFFFAOYSA-N
EDO	D [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNX	E [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.181 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.757	α = 90
b = 50.502	β = 91.6
c = 64.578	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Fraser, B.J., Dong, A., Kutera, M., Seitova, A., Li, Y., Hutchinson, A., Edwards, A., Benard, F., Levon, H., Arrowsmith, C.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN154328
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM124165

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary