SAXSdb — 4qxc

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

Lysine-specific demethylase 2A

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Histone H3.2 × 1 （P84228） N-OXALYLGLYCINE × 1 NICKEL (II) ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Histone H3.2 × 1 （P84228） N-OXALYLGLYCINE × 1 NICKEL (II) ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F6YRW4_MOUSE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–329； UniProt 36–364 Author chain C； PDBConstruct 1–329； UniProt 36–364 Author chain B； PDBConstruct 1–68； UniProt 450–517 Author chain D； PDBConstruct 1–68； UniProt 450–517

Histone H3.2

OrganismNot specified

UniProt P84228

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Lysine-specific demethylase 2A × 1 （F6YRW4） Lysine-specific demethylase 2A × 1 （F6YRW4） N-OXALYLGLYCINE × 1 NICKEL (II) ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Lysine-specific demethylase 2A × 1 （F6YRW4） Lysine-specific demethylase 2A × 1 （F6YRW4） N-OXALYLGLYCINE × 1 NICKEL (II) ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–15； UniProt 30–44 Author chain F； PDBConstruct 1–15； UniProt 30–44

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	4qxc
Deposition date deposition_date	2014-07-19
Structure title title	Crystal structure of histone demethylase KDM2A-H3K36ME2 with NOG
Keywords keywords	cupin subfamily Fe(II)/2-OG dioxygenase, JmjC domain, Histone demethylase, Oxidoreductase-Structural Protein complex; Oxidoreductase/Structural Protein
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.

4qxc__assembly_1__model_1

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

Download this curve (.dat)

4qxc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qxc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.54 Å
Rg (electron density)	21.30 Å
Total Rg	22.30 Å
Atom count	3381
Residues	409
Excluded volume	60273 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qxc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4qxc__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	Lysine-specific demethylase 2A
Molecular weight formula_weight	39031.3 kDa
EC 编号 ec_number	1.14.11.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7200

RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDME

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Lysine-specific demethylase 2A
Molecular weight formula_weight	7534.8 kDa
EC 编号 ec_number	1.14.11.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

QVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELASSDPKLALTGVPIVQWP

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H3.2
Molecular weight formula_weight	1667.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

APATGGVKKPHRYRP

Entity 4 Entity 4 non-polymer

Description description	N-OXALYLGLYCINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	446

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4qxcA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	4qxcB00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	4qxcC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	4qxcD00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	250 —

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Unit-cell length a length_a	54.603 Å
Unit-cell length b length_b	86.707 Å
Unit-cell length c length_c	170.973 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	85.490 Å
R factor r_factor	0.1760
R_work r_work	0.1745
R_free r_free	0.2035

Crystal structure of histone demethylase KDM2A-H3K36ME2 with NOG

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

Lysine-specific demethylase 2A

State in the Current Structure

Other States of the Same Protein in the Database

Histone H3.2

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

4qxc__assembly_1__model_1

4qxc__assembly_1__model_1 | I(q)

4qxc__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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of histone demethylase KDM2A-H3K36ME2 with NOG

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

Lysine-specific demethylase 2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3.2

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

4qxc__assembly_1__model_1

4qxc__assembly_1__model_1 | I(q)

4qxc__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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)