8JRD

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

PDB DOI: https://doi.org/10.2210/pdb8JRD/pdb

Classification: TRANSFERASE
Organism(s): Glycine max
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-06-16 Released: 2024-06-19
Deposition Author(s): Waki, T., Imaizumi, R., Nakata, S., Yanai, T., Takeshita, K., Sakai, N., Kataoka, K., 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: 1.83 Å
R-Value Free: 0.185
R-Value Work: 0.150
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

Waki, T., Imaizumi, R., Uno, K., Doi, Y., Tsunashima, M., Yamada, S., Mameda, R., Nakata, S., Yanai, T., Takeshita, K., Sakai, N., Kataoka, K., Yamamoto, M., Takahashi, S., Nakayama, T., Yamashita, S.

To be published.

Macromolecule Content

Total Structure Weight: 92.47 kDa
Atom Count: 6,941
Modelled Residue Count: 778
Deposited Residue Count: 808
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chalcone synthase	A, B	404	Glycine max	Mutation(s): 0 Gene Names: ICHS1
UniProt
Find proteins for Q6X0M8 (Glycine max) Explore Q6X0M8 Go to UniProtKB: Q6X0M8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6X0M8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B]	C [auth A], K [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
NAR (Subject of Investigation/LOI) Query on NAR Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B]	D [auth A], L [auth B]	NARINGENIN C₁₅ H₁₂ O₅ FTVWIRXFELQLPI-ZDUSSCGKSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain R [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth B]	O [auth B], R [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain R [auth B] Interactions & Density Focus chain O [auth B] Focus chain R [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B]	P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], Q [auth B], S [auth B], T [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS
SME Query on SME	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.185
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.61	α = 90
b = 97.47	β = 90
c = 157.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

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	22KJ1466
Japan Society for the Promotion of Science (JSPS)	Japan	22K14823
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101070

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release

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Help and Resources

8JRD

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)