SAXSdb — 1zkk

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

Histone-lysine N-methyltransferase, H4 lysine-20 specific

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Peptide corresponding to residues 15-24 of histone H4 × 4 S-ADENOSYL-L-HOMOCYSTEINE × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SET07_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–167； UniProt 231–393 Author chain B； PDBConstruct 5–167； UniProt 231–393 Author chain C； PDBConstruct 5–167； UniProt 231–393 Author chain D； PDBConstruct 5–167； UniProt 231–393

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	1zkk
Deposition date deposition_date	2005-05-03
Structure title title	Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy
Keywords keywords	pseudo-knot, histone H4, beta-sheet, TRANSFERASE; TRANSFERASE
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.

1zkk__assembly_1__model_1

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

Download this curve (.dat)

1zkk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zkk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.76 Å
Rg (electron density)	34.92 Å
Total Rg	35.21 Å
Atom count	5528
Residues	676
Excluded volume	97441 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zkk__assembly_1__model_1`	octameric （8）	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 (4)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase, H4 lysine-20 specific
Molecular weight formula_weight	18877.3 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	6545

GAMGSSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

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 polymer

Description description	Peptide corresponding to residues 15-24 of histone H4
Molecular weight formula_weight	1284.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

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

AKRHRKVLRD

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1007

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	1zkkA00
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	1zkkB00
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	1zkkC00
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	1zkkD00
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	43.960 Å
Unit-cell length b length_b	45.775 Å
Unit-cell length c length_c	94.435 Å
Unit-cell angle α angle_alpha	89.22 °
Unit-cell angle β angle_beta	87.07 °
Unit-cell angle γ angle_gamma	90.72 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	19.630 Å
R factor r_factor	0.1707
R_work r_work	0.1692
R_free r_free	0.1990

Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy

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

Histone-lysine N-methyltransferase, H4 lysine-20 specific

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

1zkk__assembly_1__model_1

1zkk__assembly_1__model_1 | I(q)

1zkk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy

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

Histone-lysine N-methyltransferase, H4 lysine-20 specific

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

1zkk__assembly_1__model_1

1zkk__assembly_1__model_1 | I(q)

1zkk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)