6CTH | pdb_00006cth

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.238 (Depositor), 0.245 (DCC)
R-Value Work:
0.208 (Depositor), 0.219 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A061FLD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE7 Query on FE7 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]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.238 (Depositor), 0.245 (DCC)
R-Value Work: 0.208 (Depositor), 0.219 (DCC)
R-Value Observed: 0.210 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

Structural Genomics Consortium (SGC)

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

Revision History (Full details and data files)

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