4MQA

Human beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)

• PDB DOI: https://doi.org/10.2210/pdb4MQA/pdb

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


• Deposited: 2013-09-16 Released: 2015-03-18 
• Deposition Author(s): White, A., Lakshminarasimhan, D., Suto, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Target-directed self-assembly of homodimeric drugs

Giardina, S.F., Pingle, M., Foreman, K.W., Werner, D.S., Bergstrom, D.E., Barany, F., Arnold, L.D.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 56.47 kDa 
• Atom Count: 4,179 
• Modelled Residue Count: 486 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptase alpha/beta-1	A, B	245	Homo sapiens	Mutation(s): 0  Gene Names: TPS1, TPS2, TPSAB1, TPSB1 EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for Q15661 (Homo sapiens) Explore Q15661  Go to UniProtKB:  Q15661
PHAROS:  Q15661 GTEx:  ENSG00000172236

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X00	F [auth B]	{(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) C44 H58 N4 O3 S2 Si2 MOGPKFKDWOMWNP-UHFFFAOYSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	C [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.168	α = 90
b = 78.168	β = 90
c = 165.458	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): White, A., Lakshminarasimhan, D., Suto, R.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary