3mo0

Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11

Method: X-RAY DIFFRACTION Dmax: 85.3 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase, H3 lysine-9 specific 5

Homo sapiens

UniProt Q9H9B1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 951–1235 Fragment:C-terminal SET domain SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 2 ZN ZINC ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;289 K;0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.78 Å R-free 0.306
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 951–1235 Fragment:C-terminal SET domain SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 1 ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;289 K;0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.78 Å R-free 0.306
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 951–1235 Chain B; UniProt 951–1235 Fragment:C-terminal SET domain SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 3 ZN ZINC ION × 10 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;289 K;0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.78 Å R-free 0.306

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

21 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EHMT1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–285; UniProt 951–1235 Author chain B; PDBConstruct 1–285; UniProt 951–1235

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3mo0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3mo0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3mo0
Deposition date deposition_date2010-04-22
Structure title titleHuman G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11
Keywords keywordsEpigenetics, Histone lysine methylation, enzymatic inhibition, lysine mimics, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.83
Radius of gyration Rg (electron density) rg_electron25.08
Forward intensity I(0) i062152900.00
Molecular weight molecular_weight57273.0 kDa
Excluded volume excluded_volume69628 ų
Envelope volume envelope_volume85983 ų
Hydration-shell volume shell_volume28926 ų
Envelope diameter envelope_diameter87.8
Shell Rg shell_rg32.07
Envelope Rg envelope_rg24.90
Shape Rg shape_rg25.10
Total Rg total_rg25.74
Total atoms total_atoms3973
Residues n_residues493
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax85.3
Rg (real space) rg_real25.83
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real6.2150e+07
I(0) uncertainty (real space) i0_real_error9.0830e+05
Rg (reciprocal space) rg_reciprocal25.83
I(0) (reciprocal space) i0_reciprocal62150000.0000
Solution quality estimate total_estimate0.6774
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary83.9
Skewness Skewness skewness0.379
Kurtosis Kurtosis kurtosis-0.195
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4732000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 0.996; Smooth: 0.956

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3mo0a_
Class classb — All beta proteins
Fold Fold foldb.85 — beta-clip
Superfamily Superfamily superfamilyb.85.7 — SET domain
Family Family familyb.85.7.0 — automated matches
Domain ID domain_idd3mo0b_
Class classb — All beta proteins
Fold Fold foldb.85 — beta-clip
Superfamily Superfamily superfamilyb.85.7 — SET domain
Family Family familyb.85.7.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3mo0A00
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology270 — Beta-clip-like
Homologous superfamily homologous superfamily10 — SET domain
Domain ID domain_id3mo0B00
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology270 — Beta-clip-like
Homologous superfamily homologous superfamily10 — SET domain

8. Citations (1)

9. Files and Curves (10)