6KHS | pdb_00006khs

Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ

• PDB DOI: https://doi.org/10.2210/pdb6KHS/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-07-16 Released: 2020-07-15 
• Deposition Author(s): Liao, S., Guo, Q., Zhu, Z.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.220 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ

Liao, S., Guo, Q., Zhu, Z.

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: 37.74 kDa 
• Atom Count: 2,701 
• Modeled Residue Count: 318 
• Deposited Residue Count: 339 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase N6AMT1	A	214	Homo sapiens	Mutation(s): 0  Gene Names: HEMK2 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
MEQ (Subject of Investigation/LOI)	C [auth A]	N5-METHYLGLUTAMINE C6 H12 N2 O3 ONXPDKGXOOORHB-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.220 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.218	α = 90
b = 110.218	β = 90
c = 130.747	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Liao, S., Guo, Q., Zhu, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31500601
National Natural Science Foundation of China	China	31501093

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description