SAXSdb — 4tn7

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 36–364 Chain B； UniProt 450–517	Fragment：UNP residues 36-364 Fragment：UNP residues 450-517	Peptide × 1 FE FE (III) ION × 1 NO NITRIC OXIDE × 1 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；100 mM Li-citrate 18-30% PEG 3350	Resolution 2.20 Å R-free 0.279
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 36–364 Chain D； UniProt 450–517	Fragment：UNP residues 36-364 Fragment：UNP residues 450-517	Peptide × 1 FE FE (III) ION × 1 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；100 mM Li-citrate 18-30% PEG 3350	Resolution 2.20 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4TN7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 36–364（329 aa） Fragment：UNP residues 36-364 Chain B 450–517（68 aa） Fragment：UNP residues 450-517	Not recorded	FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350	Resolution 1.98 Å R-free 0.237
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 36–364（329 aa） Fragment：UNP residues 36-364 Chain E 450–517（68 aa） Fragment：UNP residues 450-517	Not recorded	FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350	Resolution 1.98 Å R-free 0.237
9WSQ Structure of dimeric mouse NLRP14-KDM2A-SKP1 complex Deposited 2025-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 815–1161（347 aa） Chain E 815–1161（347 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
9WSR Structure of mouse NLRP14-KDM2A-SKP1 complex Deposited 2025-09-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 815–1161（347 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDM2A_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

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	4tn7
Deposition date deposition_date	2014-06-03
Structure title title	Crystal structure of mouse KDM2A-H3K36ME-NO complex
Keywords keywords	Oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.33 Å
Radius of gyration Rg (electron density) rg_electron	32.66 Å
Forward intensity I(0) i0	138150000.00
Molecular weight molecular_weight	95172.0 kDa
Excluded volume excluded_volume	119410 Å³
Envelope volume envelope_volume	148300 Å³
Hydration-shell volume shell_volume	38181 Å³
Envelope diameter envelope_diameter	115.0 Å
Shell Rg shell_rg	38.94 Å
Envelope Rg envelope_rg	32.65 Å
Shape Rg shape_rg	32.60 Å
Total Rg total_rg	33.35 Å
Total atoms total_atoms	6701
Residues n_residues	812
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	109.1 Å
Rg (real space) rg_real	33.44 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	1.3810e+08
I(0) uncertainty (real space) i0_real_error	2.0390e+06
Rg (reciprocal space) rg_reciprocal	33.40 Å
I(0) (reciprocal space) i0_reciprocal	138100000.0000
Solution quality estimate total_estimate	0.8806
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.8 Å
Skewness Skewness skewness	0.355
Kurtosis Kurtosis kurtosis	-0.584
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41920000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.887

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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	7113

RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDME

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 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

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Peptide
Molecular weight formula_weight	1652.9 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	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	NITRIC OXIDE
Molecular weight formula_weight	30.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 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	404

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4tn7A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	4tn7B00
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	4tn7C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	4tn7D00
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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8. Citations (1)

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Unit-cell length a length_a	55.063 Å
Unit-cell length b length_b	157.928 Å
Unit-cell length c length_c	48.706 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	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	45.166 Å
R factor r_factor	0.2320
R_work r_work	0.2294
R_free r_free	0.2794

fit	/app/data/saxs_computation/tn/4tn7/4tn7.fit
pddf	/app/data/pr_computation/tn/4tn7/4tn7.pr.out
profile	/app/data/saxs_computation/tn/4tn7/4tn7.dat

Crystal structure of mouse KDM2A-H3K36ME-NO complex

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)