SAXSdb — 4guu

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

Lysine-specific histone demethylase 1B

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 51–822	Fragment：UNP residues 51-822	Putative oxidoreductase GLYR1 × 1 （Q49A26） FA9 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(3R,3aS,7aR)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.231

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 4GUU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FWE Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A Deposited 2012-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；289 K；21% PEG3350, 200mM diammonium citrate, pH 7, EVAPORATION, temperature 289K	Resolution 2.13 Å R-free 0.246
4FWE Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A Deposited 2012-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 6 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 FLC CITRATE ANION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；289 K；21% PEG3350, 200mM diammonium citrate, pH 7, EVAPORATION, temperature 289K	Resolution 2.13 Å R-free 0.246
4FWF Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic Deposited 2012-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K	Resolution 2.70 Å R-free 0.237
4FWJ Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A Deposited 2012-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.222
4FWJ Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A Deposited 2012-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.222
4FWJ Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A Deposited 2012-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822 Chain B 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 6 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 K POTASSIUM ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.222
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822 Chain C 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.221
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 51–822（772 aa） Fragment：UNP residues 51-822 Chain D 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.221
4GU1 Crystal structure of LSD2 Deposited 2012-08-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.2M Sodium chloride, 0.1M Na/K phosphate, 7% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.94 Å R-free 0.228
4GU1 Crystal structure of LSD2 Deposited 2012-08-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.2M Sodium chloride, 0.1M Na/K phosphate, 7% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.94 Å R-free 0.228
4GU1 Crystal structure of LSD2 Deposited 2012-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822 Chain B 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 CL CHLORIDE ION × 4 NA SODIUM ION × 2 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.2M Sodium chloride, 0.1M Na/K phosphate, 7% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.94 Å R-free 0.228
4GUR Crystal structure of LSD2-NPAC with H3 in space group P21 Deposited 2012-08-29	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.51 Å R-free 0.204
4GUS Crystal structure of LSD2-NPAC with H3 in space group P3221 Deposited 2012-08-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 IOD IODIDE ION × 6 GOL GLYCEROL × 2 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1M Ammonium Iodide, 0.1M MES, 10% PEG3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.23 Å R-free 0.237
4GUT Crystal structure of LSD2-NPAC Deposited 2012-08-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 ZN ZINC ION × 3 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.207
4HSU Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 Deposited 2012-10-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.99 Å R-free 0.232
6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain K 51–822（772 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.36 Å
6R25 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 Deposited 2019-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain K 51–822（772 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.61 Å
7XE1 Crystal structure of LSD2 in complex with cis-4-Br-PCPA Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DIJ 3-(4-bromophenyl)propanal × 1 FLC CITRATE ANION × 1 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；320mM Ammonium citrate, 22% PEG 3350	Resolution 2.07 Å R-free 0.192
7XE1 Crystal structure of LSD2 in complex with cis-4-Br-PCPA Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DIJ 3-(4-bromophenyl)propanal × 1 GOL GLYCEROL × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；320mM Ammonium citrate, 22% PEG 3350	Resolution 2.07 Å R-free 0.192
7XE2 Crystal structure of LSD2 in complex with trans-4-Br-PCPA Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DIJ 3-(4-bromophenyl)propanal × 2 FLC CITRATE ANION × 1 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；300mM Ammonium citrate, 24% PEG 3350	Resolution 2.05 Å R-free 0.194
7XE2 Crystal structure of LSD2 in complex with trans-4-Br-PCPA Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DIJ 3-(4-bromophenyl)propanal × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；300mM Ammonium citrate, 24% PEG 3350	Resolution 2.05 Å R-free 0.194
7XE3 Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024) Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 8A2 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal × 1 FLC CITRATE ANION × 1 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；330mM Ammonium citrate, 26% PEG 3350	Resolution 2.82 Å R-free 0.222
7XE3 Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024) Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 8A2 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；330mM Ammonium citrate, 26% PEG 3350	Resolution 2.82 Å R-free 0.222

14 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDM1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–776； UniProt 51–822

Putative oxidoreductase GLYR1

Homo sapiens

UniProt Q49A26

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 152–268	Fragment：UNP residues 152-268	Lysine-specific histone demethylase 1B × 1 （Q8NB78） FA9 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(3R,3aS,7aR)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.231

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 4GUU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GUR Crystal structure of LSD2-NPAC with H3 in space group P21 Deposited 2012-08-29	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 152–268（117 aa） Fragment：UNP residues 152-268	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.51 Å R-free 0.204
4GUS Crystal structure of LSD2-NPAC with H3 in space group P3221 Deposited 2012-08-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 152–268（117 aa） Fragment：UNP residues 152-268	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 IOD IODIDE ION × 6 GOL GLYCEROL × 2 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1M Ammonium Iodide, 0.1M MES, 10% PEG3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.23 Å R-free 0.237
4GUT Crystal structure of LSD2-NPAC Deposited 2012-08-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 152–268（117 aa） Fragment：UNP residues 152-268	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 ZN ZINC ION × 3 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.207
4HSU Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 Deposited 2012-10-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 152–268（117 aa） Fragment：UNP residues 152-268	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.99 Å R-free 0.232
6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain L 152–268（117 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.36 Å

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

View Construct and Data Evidence

UniProt name	GLYR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 8–124； UniProt 152–268

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	4guu
Deposition date deposition_date	2012-08-29
Structure title title	Crystal structure of LSD2-NPAC with tranylcypromine
Keywords keywords	histone demethylase, 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	32.41 Å
Radius of gyration Rg (electron density) rg_electron	31.87 Å
Forward intensity I(0) i0	116323000.00
Molecular weight molecular_weight	85863.0 kDa
Excluded volume excluded_volume	107390 Å³
Envelope volume envelope_volume	133180 Å³
Hydration-shell volume shell_volume	36372 Å³
Envelope diameter envelope_diameter	116.1 Å
Shell Rg shell_rg	37.15 Å
Envelope Rg envelope_rg	32.17 Å
Shape Rg shape_rg	31.82 Å
Total Rg total_rg	32.46 Å
Total atoms total_atoms	6027
Residues n_residues	752
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	108.6 Å
Rg (real space) rg_real	32.62 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	1.1630e+08
I(0) uncertainty (real space) i0_real_error	2.0060e+06
Rg (reciprocal space) rg_reciprocal	32.54 Å
I(0) (reciprocal space) i0_reciprocal	116300000.0000
Solution quality estimate total_estimate	0.6526
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.0 Å
Skewness Skewness skewness	0.469
Kurtosis Kurtosis kurtosis	-0.422
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22300000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.905; Smooth: 0.850

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Lysine-specific histone demethylase 1B
Molecular weight formula_weight	87051.5 kDa
EC 编号 ec_number	1.-.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6246

PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Putative oxidoreductase GLYR1
Molecular weight formula_weight	13528.3 kDa
EC 编号 ec_number	1.-.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PLGSPEFSERGSKSPLKRAQEQSPRKRGRPPKDEKDLTIPESSTVKGMMAGPMAAFKWQPTASEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSITPTDK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(3R,3aS,7aR)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate ;
Molecular weight formula_weight	919.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

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8. Citations (1)

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Unit-cell length a length_a	62.820 Å
Unit-cell length b length_b	90.157 Å
Unit-cell length c length_c	87.824 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.302 Å
Low-resolution limit resolution_low	36.232 Å
R factor r_factor	0.2004
R_work r_work	0.1987
R_free r_free	0.2313

fit	/app/data/saxs_computation/gu/4guu/4guu.fit
pddf	/app/data/pr_computation/gu/4guu/4guu.pr.out
profile	/app/data/saxs_computation/gu/4guu/4guu.dat

Crystal structure of LSD2-NPAC with tranylcypromine

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

Lysine-specific histone demethylase 1B

State in the Current Structure

Other States of the Same Protein in the Database

Putative oxidoreductase GLYR1

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)