SAXSdb — 5ij7

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

Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G1KPH4_ANOCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–329； UniProt 4–332 Author chain B； PDBConstruct 1–329； UniProt 4–332

Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2

Homo sapiens

UniProt Q15910

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EZH2_HUMAN
Isoform	Q15910-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 330–643； UniProt 390–707 Author chain B； PDBConstruct 330–643； UniProt 390–707

Polycomb protein EED

Homo sapiens

UniProt O75530

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2 × 1 （G1KPH4,Q15910） Polycomb protein SUZ12 × 1 （Q15022） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2 × 1 （G1KPH4,Q15910） Polycomb protein SUZ12 × 1 （Q15022） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EED_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 2–362； UniProt 81–441 Author chain F； PDBConstruct 2–362； UniProt 81–441

Polycomb protein SUZ12

Homo sapiens

UniProt Q15022

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2 × 1 （G1KPH4,Q15910） Polycomb protein EED × 1 （O75530） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2 × 1 （G1KPH4,Q15910） Polycomb protein EED × 1 （O75530） ;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ; × 1 ZINC ION × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUZ12_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain S； PDBConstruct 11–191； UniProt 545–725 Author chain T； PDBConstruct 11–191； UniProt 545–725

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ij7
Deposition date deposition_date	2016-03-01
Structure title title	Structure of Hs/AcPRC2 in complex with a pyridone inhibitor
Keywords keywords	lysine methyltransferase, transferase-transferase inhibitor complex; transferase/transferase inhibitor
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5ij7__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ij7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ij7__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.12 Å
Rg (electron density)	33.51 Å
Total Rg	34.18 Å
Atom count	7758
Residues	947
Excluded volume	137480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ij7__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ij7__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
Molecular weight formula_weight	72941.5 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15642

MGQTGKKSEKGPICWRKRVKSEYMRLRQLKRFRRADEVKSMFNSNRQKIQERTEILNQEWKQRRIQPVHIMTSVSSLRGTRECSVTSDLDFPKQVIPLKTLNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQLDRRDEKQKNQESNQIDKESHPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFHATPNTYKRKNTEMAIDNKPCGPHCYQHLEGAKEFAAALTAENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPAPAEDVDTLGGGGSGGGGSGGGGSAAADGSSNHVYNYQPCDHPRQPCDNSCPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIEREMEIP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Polycomb protein EED
Molecular weight formula_weight	41776.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Polycomb protein SUZ12
Molecular weight formula_weight	22268.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,T

MDYKDDDDKGESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDDEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEKALETD

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 non-polymer

Description description	;5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one ;
Molecular weight formula_weight	536.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ij7E00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	5ij7F00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	69.575 Å
Unit-cell length b length_b	115.042 Å
Unit-cell length c length_c	153.033 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	91.150 Å
R factor r_factor	0.1935
R_work r_work	0.1912
R_free r_free	0.2380

Structure of Hs/AcPRC2 in complex with a pyridone inhibitor

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

Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2

State in the Current Structure

Other States of the Same Protein in the Database

Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2

State in the Current Structure

Other States of the Same Protein in the Database

Polycomb protein EED

State in the Current Structure

Other States of the Same Protein in the Database

Polycomb protein SUZ12

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ij7__assembly_1__model_1

5ij7__assembly_1__model_1 | I(q)

5ij7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Hs/AcPRC2 in complex with a pyridone inhibitor

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

Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polycomb protein EED

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polycomb protein SUZ12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ij7__assembly_1__model_1

5ij7__assembly_1__model_1 | I(q)

5ij7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)