4jds

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine

Method: X-RAY DIFFRACTION

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

Histone-lysine N-methyltransferase SETD7

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYLMETHIONINE × 2 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 2 UNKNOWN ATOM OR ION × 28 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	S-ADENOSYLMETHIONINE × 1 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNKNOWN ATOM OR ION × 8 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	S-ADENOSYLMETHIONINE × 1 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNKNOWN ATOM OR ION × 9 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	S-ADENOSYLMETHIONINE × 1 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNKNOWN ATOM OR ION × 6 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SETD7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 109–366 Author chain B； PDBConstruct 1–258； UniProt 109–366 Author chain C； PDBConstruct 1–258； UniProt 109–366 Author chain D； PDBConstruct 1–258； UniProt 109–366

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	4jds
Deposition date deposition_date	2013-02-25
Structure title title	SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine
Keywords keywords	;SETD7, SAM, PF-5426, Structural Genomics Consortium, SGC, Methyltransferase, SET domain, histone modification, transcription regulation, histone lysine methyltransferase, inhibitor, S-adenosyl-L-methionine, 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jds__assembly_1__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`4jds__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
3	1	`4jds__assembly_3__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
4	1	`4jds__assembly_4__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase SETD7
Molecular weight formula_weight	29684.0 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8940

QYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQATQQKHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide
Molecular weight formula_weight	456.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	37

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	953

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4jdsa1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4jdsa2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4jdsa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4jdsb1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4jdsb2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4jdsb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4jdsc1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4jdsc2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4jdsc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4jdsd1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d4jdsd2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d4jdsd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	4jdsA01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4jdsA02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4jdsB01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4jdsB02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4jdsC01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4jdsC02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4jdsD01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	4jdsD02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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Unit-cell length a length_a	118.048 Å
Unit-cell length b length_b	134.482 Å
Unit-cell length c length_c	137.255 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1988
R_work r_work	0.1986
R_free r_free	0.2226

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine

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

Histone-lysine N-methyltransferase SETD7

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine

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

Histone-lysine N-methyltransferase SETD7

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)