2QYO

Crystal structure of isoflavone O-methyltransferase homolog in complex with biochanin A and SAH

PDB DOI: https://doi.org/10.2210/pdb2QYO/pdb

Classification: TRANSFERASE
Organism(s): Medicago truncatula
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-08-15 Released: 2008-08-26
Deposition Author(s): Wang, C., Yu, X.-H., Liu, C.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.245
R-Value Work: 0.214

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structures of Medicago truncatula isoflavone O-methyltransferase reveal conserved surface binding motifs critical for enzymatic activity

Wang, C., Yu, X.-H., Liu, C.-J.

To be published.

Macromolecule Content

Total Structure Weight: 82.36 kDa
Atom Count: 5,869
Modelled Residue Count: 705
Deposited Residue Count: 714
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase	A, B	357	Medicago truncatula	Mutation(s): 0 Gene Names: Medicago truncatula IOMT3 gene EC: 2.1.1.46
UniProt
Find proteins for Q06YR3 (Medicago truncatula) Explore Q06YR3 Go to UniProtKB: Q06YR3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06YR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B]	K [auth A], R [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain K [auth A] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain R [auth B]
QSO Query on QSO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B]	L [auth A], S [auth B]	5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one C₁₆ H₁₂ O₅ WUADCCWRTIWANL-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain S [auth B] Interactions & Density Focus chain L [auth A] Focus chain S [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] 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 O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] 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 O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [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], O [auth B], P [auth B], Q [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] 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 O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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 O [auth B] Focus chain P [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.245
R-Value Work: 0.214
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.54	α = 90
b = 82.049	β = 101.94
c = 101.034	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Wang, C.

Yu, X.-H.

Liu, C.-J.

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description