SAXSdb — 8f8z

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

Lysine-specific demethylase PHF2

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 1–451	Not recorded	H3 N-Terminal Peptide × 1 （V9H1G0） ZN ZINC ION × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–451	Not recorded	H3 N-Terminal Peptide × 1 （V9H1G0） ZN ZINC ION × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256

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 8F8Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–70（70 aa） Fragment：PHD finger	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.78 Å R-free 0.218
3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–70（70 aa） Fragment：PHD finger	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.78 Å R-free 0.218
3PTR PHF2 Jumonji domain Deposited 2010-12-03	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 B 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	EDO 1,2-ETHANEDIOL × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.95 Å R-free 0.229
3PU3 PHF2 Jumonji domain-NOG complex Deposited 2010-12-03	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 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	OGA N-OXALYLGLYCINE × 1 EDO 1,2-ETHANEDIOL × 22 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.95 Å R-free 0.294
3PU3 PHF2 Jumonji domain-NOG complex Deposited 2010-12-03	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 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	OGA N-OXALYLGLYCINE × 1 EDO 1,2-ETHANEDIOL × 21	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.95 Å R-free 0.294
3PU8 PHF2 Jumonji-NOG-Fe(II) complex Deposited 2010-12-03	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 B 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	OXY OXYGEN MOLECULE × 1 EDO 1,2-ETHANEDIOL × 6 OGA N-OXALYLGLYCINE × 1 CL CHLORIDE ION × 1 FE FE (III) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.94 Å R-free 0.235
3PU8 PHF2 Jumonji-NOG-Fe(II) complex Deposited 2010-12-03	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 A 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	OXY OXYGEN MOLECULE × 1 EDO 1,2-ETHANEDIOL × 12 OGA N-OXALYLGLYCINE × 1 CL CHLORIDE ION × 1 FE FE (III) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.94 Å R-free 0.235
3PUA PHF2 Jumonji-NOG-Ni(II) Deposited 2010-12-03	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 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 11 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.89 Å R-free 0.210
3PUS PHF2 Jumonji-NOG-Ni(II) Deposited 2010-12-06	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 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1 NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 2.08 Å R-free 0.232
3PUS PHF2 Jumonji-NOG-Ni(II) Deposited 2010-12-06	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 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1 NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1 OXY OXYGEN MOLECULE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 2.08 Å R-free 0.232
7M10 PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1 Deposited 2021-03-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–70（70 aa） Fragment：PHD domain	Not recorded	ZN ZINC ION × 2 FMT FORMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；292 K；3.5M Sodium Formate,100mM TRIS pH 8.2	Resolution 1.15 Å R-free 0.165
8F8Y PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide Deposited 2022-11-22	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–451（451 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.06 Å R-free 0.249
8F8Y PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide Deposited 2022-11-22	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–451（451 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.06 Å R-free 0.249

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–455； UniProt 1–451 Author chain B； PDBConstruct 5–455； UniProt 1–451

H3 N-Terminal Peptide

OrganismNot specified

UniProt V9H1G0

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 E； UniProt 2–25	Non-standard monomer：Yes (specific site not provided by mmCIF)	Lysine-specific demethylase PHF2 × 1 （O75151） ZN ZINC ION × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 2–25	Non-standard monomer：Yes (specific site not provided by mmCIF)	Lysine-specific demethylase PHF2 × 1 （O75151） ZN ZINC ION × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256

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 8F8Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5SZB Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with acetylated K14 Deposited 2016-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–19（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD	Resolution 1.20 Å R-free 0.155
5SZB Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with acetylated K14 Deposited 2016-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 2–19（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD	Resolution 1.20 Å R-free 0.155
5SZC Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14 Deposited 2016-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–19（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD	Resolution 1.19 Å R-free 0.167
5Z93 Crystal Structure of SIRT3 in complex with H3K9bhb peptide Deposited 2018-02-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 7–16（10 aa） Fragment：UNP residues 7-16	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M MES pH 6.5, 25% PEG 1000	Resolution 1.95 Å R-free 0.210
5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–16（15 aa） Fragment：UNP residues 2-16	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350	Resolution 1.90 Å R-free 0.191
5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–16（15 aa） Fragment：UNP residues 2-16	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350	Resolution 1.90 Å R-free 0.191
7D87 Crystal Structure of zebrafish PHF14-PZP in complex with H3(1-25) Deposited 2020-10-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–26（25 aa） Fragment：histone H3(1-25)	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M Carboxylic acids,0.1 M Buffer System 2, 37.50% % v/v MPD_P1K_P3350 (morpheus).	Resolution 2.11 Å R-free 0.204
7D8A Crystal Structure of H3(1-13)/PHF14-PZP fusion protein Deposited 2020-10-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–13（12 aa） Fragment：H3(1-13)	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Hepes pH 7.5, 18% PEG4000, 12% isopropanol .	Resolution 2.00 Å R-free 0.212
8DS8 Crystal structure of human TNRC18 BAH domain in complex with H3K9me3 peptide Deposited 2022-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–24（23 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M Sodium Cacodylate, pH 6.5, 0.2 M Magnesium Acetate, 16-20% PEG 8000	Resolution 1.84 Å R-free 0.235
8DS8 Crystal structure of human TNRC18 BAH domain in complex with H3K9me3 peptide Deposited 2022-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–24（23 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M Sodium Cacodylate, pH 6.5, 0.2 M Magnesium Acetate, 16-20% PEG 8000	Resolution 1.84 Å R-free 0.235
8UNI LSD1-CoREST with N-formyl-FAD in complex with H3K4M histone tail Deposited 2023-10-19	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 C 2–22（21 aa） Fragment：residues 1-21 (2-22 Uniprot numbering)	Mutation：K4M	HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5	Resolution 3.40 Å R-free 0.252
8UOM LSD1-CoREST with N-formyl-FAD in complex with H3dimeK4 histone tail Deposited 2023-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–22（21 aa） Fragment：residues 1-21 (2-22 Uniprot numbering)	Non-standard monomer：Yes (specific site not provided by mmCIF)	HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5	Resolution 3.20 Å R-free 0.240

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	V9H1G0_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–24； UniProt 2–25 Author chain F； PDBConstruct 1–24； UniProt 2–25

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	8f8z
Deposition date deposition_date	2022-11-22
Structure title title	PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide
Keywords keywords	;Methyl-lysine binding; aromatic cage; plant homeodomain (PHD); Jumonji domain; plant homeodomain finger 2 (PHF2); histone H3 lysine 4 tri-methylation (H3K4me3), OXIDOREDUCTASE-TRANSFERASE complex ;; OXIDOREDUCTASE/TRANSFERASE
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	36.73 Å
Radius of gyration Rg (electron density) rg_electron	37.04 Å
Forward intensity I(0) i0	154589000.00
Molecular weight molecular_weight	97357.0 kDa
Excluded volume excluded_volume	120370 Å³
Envelope volume envelope_volume	158400 Å³
Hydration-shell volume shell_volume	38595 Å³
Envelope diameter envelope_diameter	135.6 Å
Shell Rg shell_rg	39.07 Å
Envelope Rg envelope_rg	37.24 Å
Shape Rg shape_rg	37.12 Å
Total Rg total_rg	36.88 Å
Total atoms total_atoms	6813
Residues n_residues	871
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	126.4 Å
Rg (real space) rg_real	37.21 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	1.5460e+08
I(0) uncertainty (real space) i0_real_error	2.6090e+06
Rg (reciprocal space) rg_reciprocal	36.91 Å
I(0) (reciprocal space) i0_reciprocal	154500000.0000
Solution quality estimate total_estimate	0.8014
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.3 Å
Skewness Skewness skewness	0.636
Kurtosis Kurtosis kurtosis	-0.136
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35240000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.657; Smooth: 0.610

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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 PHF2
Molecular weight formula_weight	51832.3 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	6861

GSINMATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGKSTLKKKRTWHKHGPGQAPDVKPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENASKAVRP

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	H3 N-Terminal Peptide
Molecular weight formula_weight	2632.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

ARTKQTARKSTGGKAPRKQLATKA

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	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	48

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	8f8zA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	8f8zA02
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	1360 —

Domain ID domain_id	8f8zB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	8f8zB02
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	1360 —

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8. Citations (1)

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Unit-cell length a length_a	73.854 Å
Unit-cell length b length_b	83.756 Å
Unit-cell length c length_c	104.128 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.67 °
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	monoclinic

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	54.500 Å
R factor r_factor	0.2154
R_work r_work	0.2133
R_free r_free	0.2560

fit	/app/data/saxs_computation/f8/8f8z/8f8z.fit
pddf	/app/data/pr_computation/f8/8f8z/8f8z.pr.out
profile	/app/data/saxs_computation/f8/8f8z/8f8z.dat

PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide

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

Lysine-specific demethylase PHF2

State in the Current Structure

Other States of the Same Protein in the Database

H3 N-Terminal Peptide

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

Entity 3 Entity 3 non-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)