6DUB

Crystal structure of a methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2.

Dong, C.Dong, G.Li, L.Zhu, L.Tempel, W.Liu, Y.Huang, R.Min, J.

(2018) Commun Biol 1: 183-183


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha N-terminal protein methyltransferase 1B
A, B
222Homo sapiensMutation(s): 0 
Gene Names: METTL11B (C1orf184, NRMT2)
EC: 2.1.1.299
Find proteins for Q5VVY1 (Homo sapiens)
Go to Gene View: METTL11B
Go to UniProtKB:  Q5VVY1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RCC1
E, F
6Homo sapiensMutation(s): 0 
Gene Names: RCC1 (CHC1)
Find proteins for P18754 (Homo sapiens)
Go to Gene View: RCC1
Go to UniProtKB:  P18754
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A, B, E, F
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
SAH
Query on SAH

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Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5JP
Query on 5JP
E, F
NON-POLYMERC4 H9 N O3SER
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 44.359α = 90.00
b = 44.359β = 90.00
c = 262.058γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
HKL-3000data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-11-28
    Type: Data collection, Database references