2GDD

Human beta II tryptase with inhibitor CRA-27592

• PDB DOI: https://doi.org/10.2210/pdb2GDD/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2006-03-15 Released: 2006-04-11 
• Deposition Author(s): Somoza, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.254 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 

Literature

Human beta II tryptase with inhibitor CRA-27592

Somoza, J.R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 112.28 kDa 
• Atom Count: 7,984 
• Modelled Residue Count: 972 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptase beta-2	A, B, C, D	245	Homo sapiens	Mutation(s): 0  Gene Names: TPSB2, TPS2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5AM	E [auth A], F [auth B], G [auth C], H [auth D]	BENZYL {(1S)-5-AMINO-1-[(S)-HYDROXY(5-{[4-(4-PHENYLBUTANOYL)PIPERAZIN-1-YL]METHYL}-1,2,4-OXADIAZOL-3-YL)METHYL]PENTYL}CARBAMATE C31 H42 N6 O5 LRPAFCFDXNPFAF-WNJJXGMVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.254 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.015	α = 90
b = 78.015	β = 90
c = 163.98	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): Somoza, J.R.

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary