8XE3 | pdb_00008xe3

norbelladine 4'-O-methyltransferase complexed with Mg and SAH

PDB DOI: https://doi.org/10.2210/pdb8XE3/pdb

Classification: TRANSFERASE
Organism(s): Narcissus aff. pseudonarcissus MK-2014
Expression System: Escherichia coli M15
Mutation(s): No

Deposited: 2023-12-11 Released: 2024-08-07
Deposition Author(s): Saw, Y.Y.H., Nakashima, Y., Morita, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.160 (Depositor), 0.161 (DCC)
R-Value Observed:
0.162 (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

Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases

Hnin, S.Y.Y., Nakashima, Y., Kodama, T., Morita, H.

(2024) ACS Catal : 11865-11880

DOI: https://doi.org/10.1021/acscatal.4c03305

Macromolecule Content

Total Structure Weight: 55.89 kDa
Atom Count: 4,397
Modeled Residue Count: 479
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Norbelladine 4'-O-methyltransferase	A, B	242	Narcissus aff. pseudonarcissus MK-2014	Mutation(s): 0 Gene Names: N4OMT EC: 2.1.1.336
UniProt
Find proteins for A0A077EWA5 (Narcissus aff. pseudonarcissus MK-2014) Explore A0A077EWA5 Go to UniProtKB: A0A077EWA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A077EWA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	C [auth A], D [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]