6CTH

Crystal Structure of Pathogenesis-related Protein 1G (PR-1G) Kinase Domain from Cacao

• PDB DOI: https://doi.org/10.2210/pdb6CTH/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Theobroma cacao
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-23 Released: 2018-04-11 
• Deposition Author(s): Tosarini, T.R., Profeta, G.S., dos Reis, C.V., Counago, R.M., Massirer, K.B., Edwards, A.M., Elkins, J.M., Structural Genomics Consortium (SGC)
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

Crystal Structure of Pathogenesis-related Protein 1G (PR-1G) Kinase Domain from Cacao

Tosarini, T.R., Profeta, G.S., dos Reis, C.V., Counago, R.M., Massirer, K.B., Mondego, J.M.C., Edwards, A.M., Elkins, J.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.3 kDa 
• Atom Count: 2,459 
• Modelled Residue Count: 295 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin A-like lectin protein kinase family protein	A	309	Theobroma cacao	Mutation(s): 0  Gene Names: TCM_042446
UniProt
Find proteins for A0A061FLD4 (Theobroma cacao) Explore A0A061FLD4  Go to UniProtKB:  A0A061FLD4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE7	B [auth A]	N-{(3Z)-2-oxo-3-[phenyl({4-[(piperidin-1-yl)methyl]phenyl}amino)methylidene]-2,3-dihydro-1H-indol-5-yl}ethanesulfonamide C29 H32 N4 O3 S GLDSKRNGVVYJAB-DQSJHHFOSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.798	α = 90
b = 56.798	β = 90
c = 358.04	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Tosarini, T.R., Profeta, G.S., dos Reis, C.V., Counago, R.M., Massirer, K.B., Edwards, A.M., Elkins, J.M., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description