9MYK | pdb_00009myk

A domain-swapped structure of QEVKG mutant of Monellin

• PDB DOI: https://doi.org/10.2210/pdb9MYK/pdb

• Classification: PLANT PROTEIN
• Organism(s): Dioscoreophyllum cumminsii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-21 Released: 2026-02-04 
• Deposition Author(s): Manjula, R., Subramanian, R., Gosavi, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.315 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

A domain-swapped structure of QEVKG mutant of Monellin

Manjula, R., Subramanian, R., Gosavi, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.18 kDa 
• Atom Count: 3,442 
• Modeled Residue Count: 434 
• Deposited Residue Count: 455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-chain Monellin	A, B, C, D, E	91	Dioscoreophyllum cumminsii	Mutation(s): 0
UniProt
Find proteins for P02882 (Dioscoreophyllum cumminsii) Explore P02882  Go to UniProtKB:  P02882
Find proteins for P02881 (Dioscoreophyllum cumminsii) Explore P02881  Go to UniProtKB:  P02881
UniProt Groups	P02881P02882

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.315 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.48	α = 90
b = 87.261	β = 103.41
c = 88.874	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Manjula, R., Subramanian, R., Gosavi, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release