8Z8P

norbelladine 4'-O-methyltransferase S52M variant complexed with Mg and SAH

PDB DOI: https://doi.org/10.2210/pdb8Z8P/pdb

Classification: TRANSFERASE
Organism(s): Narcissus aff. pseudonarcissus MK-2014
Expression System: Escherichia coli M15
Mutation(s): Yes

Deposited: 2024-04-22 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: 1.68 Å
R-Value Free: 0.179
R-Value Work: 0.156
R-Value Observed: 0.157

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: 112.04 kDa
Atom Count: 9,016
Modelled Residue Count: 960
Deposited Residue Count: 968
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Norbelladine 4'-O-methyltransferase	A, B, C, D	242	Narcissus aff. pseudonarcissus MK-2014	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 J [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D]	J [auth A], M [auth B], Q [auth C], S [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D]
GOL (Subject of Investigation/LOI) Query on GOL 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 K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] 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 K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], N [auth C], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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 K [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D]	I [auth A], L [auth B], P [auth C], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain R [auth D]