5N0N

Crystal structure of OphA-DeltaC6 mutant Y63F in complex with SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.188 

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
EDT
Query on EDT

Download SDF File 
Download CCD File 
A
{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
MVA
Query on MVA
A
L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.188 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.304α = 90.00
b = 93.664β = 90.00
c = 165.331γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
xia2data reduction
xia2data scaling

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