3S8J | pdb_00003s8j

Crystal structure of a papaya latex serine protease inhibitor (PPI) at 2.6A resolution

PDB DOI: https://doi.org/10.2210/pdb3S8J/pdb

Classification: HYDROLASE INHIBITOR
Organism(s): Carica papaya
Mutation(s): No

Deposited: 2011-05-29 Released: 2011-11-02
Deposition Author(s): Garcia-Pino, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.213 (Depositor), 0.206 (DCC)
R-Value Work:
0.150 (Depositor), 0.148 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The plasticity of the beta-Trefoil fold constitutes an evolutionary platform for protease inhibition

Azarkan, M., Martinez-Rodriguez, S., Buts, L., Baeyens-Volant, D., Garcia-Pino, A.

(2011) J Biological Chem 286: 43726-43734

PubMed: 22027836 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M111.291310
Primary Citation Related Structures:
3S8J, 3S8K

PubMed Abstract:
Proteases carry out a number of crucial functions inside and outside the cell. To protect the cells against the potentially lethal activities of these enzymes, specific inhibitors are produced to tightly regulate the protease activity. Independent reports suggest that the Kunitz-soybean trypsin inhibitor (STI) family has the potential to inhibit proteases with different specificities. In this study, we use a combination of biophysical methods to define the structural basis of the interaction of papaya protease inhibitor (PPI) with serine proteases. We show that PPI is a multiple-headed inhibitor; a single PPI molecule can bind two trypsin units at the same time. Based on sequence and structural analysis, we hypothesize that the inherent plasticity of the β-trefoil fold is paramount in the functional evolution of this family toward multiple protease inhibition.

Organizational Affiliation

Protein Chemistry Unit, Faculty of Medicine, Université Libre de Bruxelles, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels, Belgium.

Macromolecule Content

Total Structure Weight: 42.29 kDa
Atom Count: 2,911
Modeled Residue Count: 363
Deposited Residue Count: 368
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Latex serine proteinase inhibitor	A, B	184	Carica papaya	Mutation(s): 0
UniProt
Find proteins for P80691 (Carica papaya) Explore P80691 Go to UniProtKB: P80691
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80691
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.213 (Depositor), 0.206 (DCC)
R-Value Work: 0.150 (Depositor), 0.148 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.699	α = 90
b = 74.699	β = 90
c = 78.97	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-11-02

Deposition Author(s):

Garcia-Pino, A.

Revision History (Full details and data files)

Version 1.0: 2011-11-02
Type: Initial release
Version 1.1: 2013-06-19
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Structure summary