9QFV | pdb_00009qfv

Human Tryptase beta-2 (hTPSB2)

PDB DOI: https://doi.org/10.2210/pdb9QFV/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2025-03-12 Released: 2025-03-26
Deposition Author(s): Porta, A., Manelfi, C., Talarico, C., Beccari, A.R., Brindisi, M., Summa, V., Iaconis, D., Gobbi, M., Beeg, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.219 (Depositor), 0.227 (DCC)
R-Value Work:
0.188 (Depositor), 0.195 (DCC)
R-Value Observed:
0.188 (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

Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors

Porta, A., Manelfi, C., Talarico, C., Beccari, A.R., Brindisi, M., Summa, V., Iaconis, D., Gobbi, M., Beeg, M.

(2025) Molecules

DOI: https://doi.org/10.3390/molecules30061338

Macromolecule Content

Total Structure Weight: 113.4 kDa
Atom Count: 8,560
Modelled Residue Count: 976
Deposited Residue Count: 980
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptase beta-2	A, B, C, D	245	Homo sapiens	Mutation(s): 0 EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for P20231 (Homo sapiens) Explore P20231 Go to UniProtKB: P20231
PHAROS: P20231 GTEx: ENSG00000197253
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20231
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE (Subject of Investigation/LOI) Query on 1PE Download Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain Q [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain Q [auth B]	JA [auth D], Q [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain JA [auth D] Focus chain Q [auth B]
MES (Subject of Investigation/LOI) Query on MES Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain KA [auth D] SDF format, chain U [auth B] SDF format, chain X [auth C] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain X [auth C]	J [auth A], KA [auth D], U [auth B], X [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain KA [auth D] Focus chain U [auth B] Focus chain X [auth C] Interactions & Density Focus chain J [auth A] Focus chain KA [auth D] Focus chain U [auth B] Focus chain X [auth C]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	CA [auth C] G [auth A] GA [auth D] HA [auth D] N [auth A] CA [auth C], G [auth A], GA [auth D], HA [auth D], N [auth A], R [auth B], S [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain I [auth A] SDF format, chain MA [auth D] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain W [auth B]	AA [auth C], I [auth A], MA [auth D], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain I [auth A] Focus chain MA [auth D] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain I [auth A] Focus chain MA [auth D] Focus chain W [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain IA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain IA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain IA [auth D]	BA [auth C] DA [auth C] F [auth A] FA [auth D] H [auth A] BA [auth C], DA [auth C], F [auth A], FA [auth D], H [auth A], IA [auth D], K [auth A], L [auth A], LA [auth D], M [auth A], P [auth B], T [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain H [auth A] Focus chain IA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain P [auth B] Focus chain T [auth B] Focus chain V [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain H [auth A] Focus chain IA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain P [auth B] Focus chain T [auth B] Focus chain V [auth B]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain O [auth B] SDF format, chain Y [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth C]	E [auth A], EA [auth D], O [auth B], Y [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain EA [auth D] Focus chain O [auth B] Focus chain Y [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth D] Focus chain O [auth B] Focus chain Y [auth C]