3CKK

Crystal structure of human methyltransferase-like protein 1

• PDB DOI: https://doi.org/10.2210/pdb3CKK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-16 Released: 2008-04-01 
• Deposition Author(s): Dong, A., Zeng, H., Dobrovetsky, E., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.218 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Crystal structure of human methyltransferase-like protein 1.

Zeng, H., Dong, A., Dobrovetsky, E., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.53 kDa 
• Atom Count: 1,809 
• Modelled Residue Count: 196 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(7)-)-methyltransferase	A	235	Homo sapiens	Mutation(s): 0  Gene Names: METTL1, C12orf1 EC: 2.1.1.33 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBP6 (Homo sapiens) Explore Q9UBP6  Go to UniProtKB:  Q9UBP6
PHAROS:  Q9UBP6 GTEx:  ENSG00000037897

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.218 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.316	α = 90
b = 90.316	β = 90
c = 54.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Dong, A., Zeng, H., Dobrovetsky, E., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description