5V9I | pdb_00005v9i

Crystal structure of catalytic domain of G9a with MS0105

• PDB DOI: https://doi.org/10.2210/pdb5V9I/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-23 Released: 2018-03-21 
• Deposition Author(s): Dong, A., Zeng, H., Liu, J., Xiong, Y., Babault, N., Jin, J., Walker, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Wu, H., Brown, P.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.275 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of catalytic domain of G9a with MS0105

Zeng, H., Dong, A., Liu, J., Xiong, Y., Babault, N., Jin, J., Walker, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Wu, H., Brown, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.6 kDa 
• Atom Count: 9,547 
• Modeled Residue Count: 1,064 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase EHMT2	A, B, C, D	283	Homo sapiens	Mutation(s): 0  Gene Names: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.367 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KQ7 (Homo sapiens) Explore Q96KQ7  Go to UniProtKB:  Q96KQ7
PHAROS:  Q96KQ7 GTEx:  ENSG00000204371

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
90P	EA [auth C], J [auth A], MA [auth D], T [auth B]	N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine C24 H37 N5 O2 ROYAWJTXZUOQDE-UHFFFAOYSA-N
SAM	DA [auth C], I [auth A], LA [auth D], S [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL	FA [auth C], K [auth A], L [auth A], M [auth A], NA [auth D], OA [auth D], U [auth B], V [auth B], W [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	AA [auth C], BA [auth C], CA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], HA [auth D], IA [auth D], JA [auth D], KA [auth D], O [auth B], P [auth B], Q [auth B], R [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	GA [auth C], N [auth A], X [auth B], Y [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.275 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.234 (Depositor) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.607	α = 90
b = 77.509	β = 91.41
c = 134.794	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Dong, A., Zeng, H., Liu, J., Xiong, Y., Babault, N., Jin, J., Walker, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Wu, H., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description