38KF | pdb_000038kf

Crystal Structure of Chalcone Isomerase from Medicago Truncatula Complexed with Phloretin

PDB DOI: https://doi.org/10.2210/pdb38KF/pdb

Classification: PLANT PROTEIN
Organism(s): Medicago truncatula
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2026-08-31 Released: 2026-09-16
Deposition Author(s): Burke, J.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.249 (Depositor), 0.251 (DCC)
R-Value Work:
0.220 (Depositor), 0.221 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Snapshots from the Catalytic Landscape of Chalcone Isomerase

Burke, J.R., Rangel, M.A., Vasquez Meza, V.I., Mims, H.N., Darko, T.O., Ixcoy, K., Ruiz Rivera, A., Zhang, J., Wolf-Saxon, E.R.

To be published.

Macromolecule Content

Total Structure Weight: 197.1 kDa
Atom Count: 13,416
Modeled Residue Count: 1,686
Deposited Residue Count: 1,792
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone-flavonone isomerase family protein	A, B, C, D, E A, B, C, D, E, F, G, H	224	Medicago truncatula	Mutation(s): 0 Gene Names: 11445536, MTR_1g115870
UniProt
Find proteins for B7FJK3 (Medicago truncatula) Explore B7FJK3 Go to UniProtKB: B7FJK3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7FJK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G50 (Subject of Investigation/LOI) Query on G50 Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	3-(4-HYDROXYPHENYL)-1-(2,4,6-TRIHYDROXYPHENYL)PROPAN-1-ONE C₁₅ H₁₄ O₅ VGEREEWJJVICBM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]