8XDP

O-methyltransferase from Lycoris longituba complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
norbelladine O-methyltransferase
A, B
242Lycoris longitubaMutation(s): 0 
EC: 2.1.1.336
UniProt
Find proteins for A0A6B9TNK2 (Lycoris longituba)
Explore A0A6B9TNK2 
Go to UniProtKB:  A0A6B9TNK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6B9TNK2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
H6N (Subject of Investigation/LOI)
Query on H6N

Download Ideal Coordinates CCD File 
F [auth B]Protocatechuic aldehyde
C7 H6 O3
IBGBGRVKPALMCQ-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.781α = 90
b = 81.421β = 90
c = 118.454γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP22H02777
Japan Society for the Promotion of Science (JSPS)JapanJP22K15303

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release