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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 ?
R-Value Free:
0.275 (Depositor), 0.270 (DCC)
R-Value Work:
0.234 (Depositor), 0.230 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96KQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
90P Query on 90P Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain EA [auth C] SDF format, chain J [auth A] SDF format, chain MA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth D]	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		Interactions Focus chain EA [auth C] Focus chain J [auth A] Focus chain MA [auth D] Focus chain T [auth B] Interactions & Density Focus chain EA [auth C] Focus chain J [auth A] Focus chain MA [auth D] Focus chain T [auth B]
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain LA [auth D] SDF format, chain S [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain S [auth B]	DA [auth C], I [auth A], LA [auth D], S [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain DA [auth C] Focus chain I [auth A] Focus chain LA [auth D] Focus chain S [auth B] Interactions & Density Focus chain DA [auth C] Focus chain I [auth A] Focus chain LA [auth D] Focus chain S [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain L [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain L [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain L [auth A]	FA [auth C] K [auth A] L [auth A] M [auth A] NA [auth D] 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		Interactions Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain HA [auth D] SDF format, chain KA [auth D] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain Z [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain P [auth B] SDF format, chain R [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B]	AA [auth C] BA [auth C] CA [auth C] E [auth A] F [auth A] 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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Z [auth C]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain N [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	GA [auth C], N [auth A], X [auth B], Y [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain GA [auth C] Focus chain N [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain GA [auth C] Focus chain N [auth A] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 ?
R-Value Free: 0.275 (Depositor), 0.270 (DCC)
R-Value Work: 0.234 (Depositor), 0.230 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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