5N0R

Crystal structure of OphA-DeltaC6 mutant Y66F in complex with SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds.

Song, H.van der Velden, N.S.Shiran, S.L.Bleiziffer, P.Zach, C.Sieber, R.Imani, A.S.Krausbeck, F.Aebi, M.Freeman, M.F.Riniker, S.Kunzler, M.Naismith, J.H.

(2018) Sci Adv 4: eaat2720-eaat2720


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide N-methyltransferase
A
410N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MVA
Query on MVA
A
L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.178 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.652α = 90.00
b = 93.355β = 90.00
c = 165.355γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
xia2data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references