8JCR | pdb_00008jcr

Crystal structure of Calotropain FI from Calotropis gigantea (pH 6.0)

PDB DOI: https://doi.org/10.2210/pdb8JCR/pdb

Classification: HYDROLASE
Organism(s): Calotropis gigantea
Mutation(s): No

Deposited: 2023-05-11 Released: 2024-05-22
Deposition Author(s): Kumar, A., Jamdar, S.N., Srivastava, G., Makde, R.D.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 ?
R-Value Free:
0.175 (Depositor), 0.172 (DCC)
R-Value Work:
0.158 (Depositor), 0.155 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Papain-Like Cysteine Protease, Calotropain FI, Purified from the Latex of Calotropis gigantea.

Jamdar, S.N., Kumar, A., Srivastava, G., Makde, R.D.

(2025) J Agric Food Chem

PubMed: 40036158 Search on PubMed
DOI: https://doi.org/10.1021/acs.jafc.4c10898
Primary Citation of Related Structures:
8JCQ, 8JCR

PubMed Abstract:
The latex of Calotropis gigantea and Calotropis procera elute as two distinct peaks on cation exchange chromatography. One of the peaks is reported to possess multiple papain-like cysteine proteases with different biochemical properties that have been identified with different names. This is mainly due to the absence of a primary sequence for the proteases. Here, we report the crystal structures of calotropain FI from C. gigantea bound to the inhibitor E64 at pH 6 and 9 at 1.25 and 1.4 ?, respectively. Both structures are identical and are very similar to ervatamin B and papain structures. The high quality of electron density maps revealed the primary sequence of calotropain FI. The sequence comparison shows that calotropain FI from C. gigantea is orthologous to procerain, CpCp1-3, and SnuCalCp03 from C. procera and rather distinct from procerain B.

Organizational Affiliation

Food Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.

Macromolecule Content

Total Structure Weight: 23.88 kDa
Atom Count: 1,922
Modelled Residue Count: 214
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Procerain, Calotropain FI	A	214	Calotropis gigantea	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E64 (Subject of Investigation/LOI) Query on E64 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C₁₅ H₃₀ N₅ O₅ QPQNJAXBPHVASB-QWRGUYRKSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 ?
R-Value Free: 0.175 (Depositor), 0.172 (DCC)
R-Value Work: 0.158 (Depositor), 0.155 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 68.675	α = 90
b = 120.98	β = 90
c = 61.024	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	India	--

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release
Version 2.0: 2024-11-20
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Structure summary
Version 2.1: 2025-03-19
Changes: Database references