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	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	Histone H3.2 × 1 （P84228） OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M CITRATE NA 18% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.204
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	Histone H3.2 × 1 （P84228） OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M CITRATE NA 18% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.204

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 4QXC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4QWN Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure Deposited 2014-07-16	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	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.264
4QWN Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure Deposited 2014-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–364（329 aa） Fragment：UNP residues 36-364 Chain D 450–517（68 aa） Fragment：UNP residues 450-517	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.264
4QX7 Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg Deposited 2014-07-18	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	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M Na citrate, 18-22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.34 Å R-free 0.258
4QX7 Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg Deposited 2014-07-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–364（329 aa） Fragment：UNP residues 36-364 Chain D 450–517（68 aa） Fragment：UNP residues 450-517	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M Na citrate, 18-22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.34 Å R-free 0.258
4QX8 Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg Deposited 2014-07-19	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	NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Na Citrate, 18-20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.227
4QX8 Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg Deposited 2014-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–364（329 aa） Fragment：UNP residues 36-364 Chain D 450–517（68 aa） Fragment：UNP residues 450-517	Not recorded	NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Na Citrate, 18-20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.227
4QXB crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG Deposited 2014-07-19	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	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.207
4QXB crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG Deposited 2014-07-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–364（329 aa） Fragment：UNP residues 36-364 Chain D 450–517（68 aa） Fragment：UNP residues 450-517	Not recorded	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.207
4QXH Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG Deposited 2014-07-20	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	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.243
4QXH Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG Deposited 2014-07-20	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–364（329 aa） Fragment：UNP residues 36-364 Chain D 450–517（68 aa） Fragment：UNP residues 450-517	Not recorded	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.243

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

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	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 E； UniProt 30–44	Fragment：UNP residues 30-44 Non-standard monomer：Yes (specific site not provided by mmCIF)	Lysine-specific demethylase 2A × 1 （F6YRW4） Lysine-specific demethylase 2A × 1 （F6YRW4） OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M CITRATE NA 18% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.204
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 30–44	Fragment：UNP residues 30-44 Non-standard monomer：Yes (specific site not provided by mmCIF)	Lysine-specific demethylase 2A × 1 （F6YRW4） Lysine-specific demethylase 2A × 1 （F6YRW4） OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M CITRATE NA 18% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.204

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 4QXC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V86 Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide Deposited 2007-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–10（9 aa） Fragment：H3 (1-21), BIOTINILATED AT C-TERMINUS	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 28% PEG 20,000, 0.1M MES PH 6.5, 3% ISOPROPANOL TEMPERATURE 293K	Resolution 2.05 Å R-free 0.211
2V86 Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide Deposited 2007-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–10（9 aa） Fragment：H3 (1-21), BIOTINILATED AT C-TERMINUS	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 28% PEG 20,000, 0.1M MES PH 6.5, 3% ISOPROPANOL TEMPERATURE 293K	Resolution 2.05 Å R-free 0.211
2V87 Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide Deposited 2007-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–14（13 aa） Fragment：H3 (1-21), BIOTINYLATED AT C-TERMINUS, UNP RESIDUES 2-14	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM OF POTASSIUM FORMATE. TEMPERATURE 293K	Resolution 1.80 Å R-free 0.208
2V87 Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide Deposited 2007-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–14（13 aa） Fragment：H3 (1-21), BIOTINYLATED AT C-TERMINUS, UNP RESIDUES 2-14	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM OF POTASSIUM FORMATE. TEMPERATURE 293K	Resolution 1.80 Å R-free 0.208
4QWN Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure Deposited 2014-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.264
4QWN Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure Deposited 2014-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.264
4QX7 Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg Deposited 2014-07-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M Na citrate, 18-22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.34 Å R-free 0.258
4QX7 Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg Deposited 2014-07-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M Na citrate, 18-22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.34 Å R-free 0.258
4QX8 Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg Deposited 2014-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Na Citrate, 18-20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.227
4QX8 Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg Deposited 2014-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Na Citrate, 18-20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.227
4QXB crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG Deposited 2014-07-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.207
4QXB crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG Deposited 2014-07-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.207
4QXH Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG Deposited 2014-07-20	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.243
4QXH Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG Deposited 2014-07-20	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.243

7 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

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

Radius of gyration Rg (Guinier) rg_guinier	31.38 Å
Radius of gyration Rg (electron density) rg_electron	30.33 Å
Forward intensity I(0) i0	140664000.00
Molecular weight molecular_weight	95643.0 kDa
Excluded volume excluded_volume	119930 Å³
Envelope volume envelope_volume	144920 Å³
Hydration-shell volume shell_volume	39418 Å³
Envelope diameter envelope_diameter	107.7 Å
Shell Rg shell_rg	37.92 Å
Envelope Rg envelope_rg	30.25 Å
Shape Rg shape_rg	30.26 Å
Total Rg total_rg	31.16 Å
Total atoms total_atoms	6727
Residues n_residues	814
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	100.1 Å
Rg (real space) rg_real	31.36 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.4070e+08
I(0) uncertainty (real space) i0_real_error	2.0050e+06
Rg (reciprocal space) rg_reciprocal	31.37 Å
I(0) (reciprocal space) i0_reciprocal	140700000.0000
Solution quality estimate total_estimate	0.9015
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.0 Å
Skewness Skewness skewness	0.296
Kurtosis Kurtosis kurtosis	-0.524
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51350000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

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	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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/qx/4qxc/4qxc.fit
pddf	/app/data/pr_computation/qx/4qxc/4qxc.pr.out
profile	/app/data/saxs_computation/qx/4qxc/4qxc.dat

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

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 (6)

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 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)