6I5Z | pdb_00006i5z

Papaver somniferum O-methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb6I5Z/pdb

• Classification: TRANSFERASE
• Organism(s): Papaver somniferum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-15 Released: 2019-03-27 
• Deposition Author(s): Davies, G.J., Cabry, M.P., Offen, W.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.289 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of Papaver somniferum O-Methyltransferase 1 Reveals Initiation of Noscapine Biosynthesis with Implications for Plant Natural Product Methylation

Cabry, M.P., Offen, W.A., Winzer, T.H., Li, Y., Graham, I.A., Davies, G.J., Saleh, P.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b01038

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 172.72 kDa 
• Atom Count: 10,191 
• Modeled Residue Count: 1,380 
• Deposited Residue Count: 1,572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase 1	A, B, C, D	393	Papaver somniferum	Mutation(s): 0  Gene Names: MT1 EC: 2.1.1.89 (UniProt), 2.1.1.117 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for I3V6A7 (Papaver somniferum) Explore I3V6A7  Go to UniProtKB:  I3V6A7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	G [auth D]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SAH	E [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.289 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.148	α = 90
b = 111.148	β = 90
c = 302.38	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Davies, G.J., Cabry, M.P., Offen, W.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M011151/1

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-04-10
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2025-12-10
  Changes: Data collection, Structure summary