SAXSdb — 4uc4

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

Lysine-specific demethylase 4B

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	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDM4B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–119； UniProt 917–1031 Author chain B； PDBConstruct 5–119； UniProt 917–1031

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	4uc4
Deposition date deposition_date	2014-08-13
Structure title title	Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B
Keywords keywords	chromatin, tudor, REPLICATION; REPLICATION
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.

4uc4__assembly_1__model_1

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

Download this curve (.dat)

4uc4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4uc4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.03 Å
Rg (electron density)	21.30 Å
Total Rg	22.04 Å
Atom count	1716
Residues	218
Excluded volume	30264 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4uc4__assembly_1__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4uc4a1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.0 — automated matches

Domain ID domain_id	d4uc4a2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.0 — automated matches

Domain ID domain_id	d4uc4b1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.0 — automated matches

Domain ID domain_id	d4uc4b2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	4uc4A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	4uc4A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4uc4B01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	4uc4B02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	70 —

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Unit-cell length a length_a	77.436 Å
Unit-cell length b length_b	77.436 Å
Unit-cell length c length_c	50.758 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.561 Å
Low-resolution limit resolution_low	27.977 Å
R factor r_factor	0.2034
R_work r_work	0.1973
R_free r_free	0.2544

Description description	Lysine-specific demethylase 4B
Molecular weight formula_weight	13374.8 kDa
EC 编号 ec_number	1.14.11.-
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1782

Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B

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

Lysine-specific demethylase 4B

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

4uc4__assembly_1__model_1

4uc4__assembly_1__model_1 | I(q)

4uc4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B

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

Lysine-specific demethylase 4B

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

4uc4__assembly_1__model_1

4uc4__assembly_1__model_1 | I(q)

4uc4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)