3TC2 | pdb_00003tc2

Crystal structure of potato serine protease inhibitor.

PDB DOI: https://doi.org/10.2210/pdb3TC2/pdb

Classification: Hydrolase Inhibitor
Organism(s): Solanum tuberosum
Mutation(s): No

Deposited: 2011-08-08 Released: 2012-06-20
Deposition Author(s): Meulenbroek, E.M., Thomassen, E.A.J., Pannu, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.168 (Depositor), 0.167 (DCC)
R-Value Observed:
0.171 (Depositor)

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This is version 1.2 of the entry. See complete history.

Literature

Structure of a post-translationally processed heterodimeric double-headed Kunitz-type serine protease inhibitor from potato.

Meulenbroek, E.M., Thomassen, E.A., Pouvreau, L., Abrahams, J.P., Gruppen, H., Pannu, N.S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 794-799

PubMed: 22751664 Search on PubMed
DOI: https://doi.org/10.1107/S090744491201222X
Primary Citation Related Structures:
3TC2

PubMed Abstract:
Potato serine protease inhibitor (PSPI) constitutes about 22% of the total amount of proteins in potato tubers (cv. Elkana), making it the most abundant protease inhibitor in the plant. PSPI is a heterodimeric double-headed Kunitz-type serine protease inhibitor that can tightly and simultaneously bind two serine proteases by mimicking the substrate of the enzyme with its reactive-site loops. Here, the crystal structure of PSPI is reported, representing the first heterodimeric double-headed Kunitz-type serine protease inhibitor structure to be determined. PSPI has a β-trefoil fold and, based on the structure, two reactive-site loops bearing residues Phe75 and Lys95 were identified.

Organizational Affiliation

Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.

Macromolecule Content

Total Structure Weight: 60.97 kDa
Atom Count: 4,642
Modeled Residue Count: 536
Deposited Residue Count: 561
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kunitz-type proteinase inhibitor P1H5	A, B, C	187	Solanum tuberosum	Mutation(s): 0
UniProt
Find proteins for Q8S380 (Solanum tuberosum) Explore Q8S380 Go to UniProtKB: Q8S380
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8S380
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.168 (Depositor), 0.167 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.822	α = 90
b = 93.92	β = 100.69
c = 55.442	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-20

Deposition Author(s):

Meulenbroek, E.M.

Thomassen, E.A.J.

Revision History (Full details and data files)

Version 1.0: 2012-06-20
Type: Initial release
Version 1.1: 2014-04-16
Changes: Database references
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.