6K0X | pdb_00006k0x

Structure of N6AMT1-TRMT112 Complex with SAM

• PDB DOI: https://doi.org/10.2210/pdb6K0X/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2019-05-07 Released: 2019-06-05 
• Deposition Author(s): Guo, Q., Liao, S., Xu, C., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Models: experimental

Literature

Structure of HEMK2-TRM112 Complex with SAM

Guo, Q., Liao, S., Xu, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.66 kDa 
• Atom Count: 2,574 
• Modeled Residue Count: 318 
• Deposited Residue Count: 341 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase N6AMT1	A	216	Homo sapiens	Mutation(s): 0  Gene Names: N6AMT1 EC: 2.1.1 (PDB Primary Data), 2.1.1.72 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5N5 (Homo sapiens) Explore Q9Y5N5  Go to UniProtKB:  Q9Y5N5
PHAROS:  Q9Y5N5 GTEx:  ENSG00000156239

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional methyltransferase subunit TRM112-like protein	B	125	Homo sapiens	Mutation(s): 0  Gene Names: TRMT112
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI30 (Homo sapiens) Explore Q9UI30  Go to UniProtKB:  Q9UI30
PHAROS:  Q9UI30 GTEx:  ENSG00000173113

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.607	α = 90
b = 109.607	β = 90
c = 130.368	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Guo, Q., Liao, S., Xu, C., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description