9KAH | pdb_00009kah

Crystal Structure of Chalcone Syntase and Chalcone Isomerase-like Protein Complex from Physcomitrella patens

PDB DOI: https://doi.org/10.2210/pdb9KAH/pdb

Classification: TRANSFERASE
Organism(s): Physcomitrium patens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-10-28 Released: 2025-10-29
Deposition Author(s): Imaizumi, R., Waki, T., Yasuda, A., Yanai, T., Takeshita, K., Sakai, N., Yamamoto, M., Nakayama, T., Yamashita, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.213 (Depositor), 0.216 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis, dynamics, and mode of action of enhancer of flavonoid production in metabolon

Imaizumi, R., Waki, T., Yasuda, A., Yanai, T., Takeshita, K., Sakai, N., Yamamoto, M., Nakayama, T., Yamashita, S.

To be published.

Macromolecule Content

Total Structure Weight: 280.4 kDa
Atom Count: 20,998
Modeled Residue Count: 2,379
Deposited Residue Count: 2,564
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone synthase	A, B, E, F	413	Physcomitrium patens	Mutation(s): 0 Gene Names: PHYPA_029015 EC: 2.3.1.74
UniProt
Find proteins for Q2VAZ3 (Physcomitrium patens) Explore Q2VAZ3 Go to UniProtKB: Q2VAZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2VAZ3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone-flavonone isomerase family protein	C, D, G, H	228	Physcomitrium patens	Mutation(s): 0 Gene Names: PHYPA_006757
UniProt
Find proteins for A9SRW1 (Physcomitrium patens) Explore A9SRW1 Go to UniProtKB: A9SRW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9SRW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain I [auth B] MOL2 format, chain M [auth H] MOL2 format, chain I [auth B] mmCIF format, chain M [auth H] mmCIF format, chain I [auth B]	I [auth B], M [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain M [auth H] Interactions & Density Focus chain I [auth B] Focus chain M [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth G] SDF format, chain K [auth D] SDF format, chain J [auth C] MOL2 format, chain L [auth G] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] mmCIF format, chain L [auth G] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C]	J [auth C], K [auth D], L [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth G] Interactions & Density Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, E, F	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.213 (Depositor), 0.216 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.9	α = 74.438
b = 88.87	β = 74.318
c = 117.97	γ = 68.803

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23H05470
Japan Society for the Promotion of Science (JSPS)	Japan	21H02115
Japan Society for the Promotion of Science (JSPS)	Japan	24K23286
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101070