SAXSdb — 5fp3

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

HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid × 1 ZINC ION × 1 MAGNESIUM ION × 2 BICINE × 2 COBALT (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid × 1 ZINC ION × 1 MAGNESIUM ION × 2 BICINE × 2 COBALT (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDM6B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–504； UniProt 1141–1643 Author chain B； PDBConstruct 2–504； UniProt 1141–1643

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	5fp3
Deposition date deposition_date	2015-11-27
Structure title title	Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases
Keywords keywords	OXIDOREDUCTASE, INHIBITOR, JMJD3, KDM6B, JUMONJI; OXIDOREDUCTASE
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.

5fp3__assembly_1__model_1

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

Download this curve (.dat)

5fp3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fp3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.01 Å
Rg (electron density)	23.11 Å
Total Rg	23.97 Å
Atom count	3499
Residues	435
Excluded volume	62058 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fp3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5fp3__assembly_2__model_1`	monomeric （1）	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 (7)

Entity 1 Entity 1 polymer

Description description	HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
Molecular weight formula_weight	58050.3 kDa
EC 编号 ec_number	1.14.11.-
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	7843

MDVVRASRNAKVKGKFRESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEKESEDEESEEPDSTTGTPPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAPASTSRHHHHHH

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 non-polymer

Description description	3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid
Molecular weight formula_weight	284.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	BICINE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	835

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5fp3A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	5fp3A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1370 —

Domain ID domain_id	5fp3A03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5fp3B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	5fp3B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1370 —

Domain ID domain_id	5fp3B03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	61.199 Å
Unit-cell length b length_b	65.552 Å
Unit-cell length c length_c	77.301 Å
Unit-cell angle α angle_alpha	85.59 °
Unit-cell angle β angle_beta	67.65 °
Unit-cell angle γ angle_gamma	68.39 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	71.300 Å
R factor r_factor	0.2062
R_work r_work	0.2046
R_free r_free	0.2432

Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases

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

HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3

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

5fp3__assembly_1__model_1

5fp3__assembly_1__model_1 | I(q)

5fp3__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases

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

HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3

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

5fp3__assembly_1__model_1

5fp3__assembly_1__model_1 | I(q)

5fp3__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)