7dyv

Human JMJD5 in complex with MN and 5-(benzylamino)pyridine-2,4-dicarboxylic acid.

Method: X-RAY DIFFRACTION D_max: 59.1 Å Quality: GOOD

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

Bifunctional peptidase and arginyl-hydroxylase JMJD5

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 183–416	Not recorded	MN MANGANESE (II) ION × 1 HRF 5-(benzylamino)pyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride	Resolution 1.92 Å R-free 0.240

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 7DYV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UYJ Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG Deposited 2011-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 173–416（244 aa） Fragment：Catalytic core domain, UNP residues 173-416 Chain B 173–416（244 aa） Fragment：Catalytic core domain, UNP residues 173-416	Not recorded	NI NICKEL (II) ION × 2 AKG 2-OXOGLUTARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；291 K；8% PEG3350, 0.1M HepesNa pH 7.5, EVAPORATION, temperature 291K	Resolution 2.35 Å R-free 0.253
4AAP Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG) Deposited 2011-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–454（237 aa） Fragment：JMJD5 DOMAIN, RESIDUES 218-454	Not recorded	ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 16% PEG_3350, 0.007M NICL, 0M CDCL, 0.007M MGCL, 0.1M HEPES PH 7.3	Resolution 2.60 Å R-free 0.253
4AAP Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG) Deposited 2011-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 218–454（237 aa） Fragment：JMJD5 DOMAIN, RESIDUES 218-454	Not recorded	ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 16% PEG_3350, 0.007M NICL, 0M CDCL, 0.007M MGCL, 0.1M HEPES PH 7.3	Resolution 2.60 Å R-free 0.253
4GAZ Crystal Structure of a Jumonji Domain-containing Protein JMJD5 Deposited 2012-07-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 176–416（241 aa） Fragment：JmjC domain, UNP residues 176-416	Not recorded	NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；289 K；100mM HEPES, 9% PEG 3350 (w/v), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.81 Å R-free 0.274
4GAZ Crystal Structure of a Jumonji Domain-containing Protein JMJD5 Deposited 2012-07-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 176–416（241 aa） Fragment：JmjC domain, UNP residues 176-416	Not recorded	NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；289 K；100mM HEPES, 9% PEG 3350 (w/v), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.81 Å R-free 0.274
4GJY JMJD5 in complex with N-Oxalylglycine Deposited 2012-08-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa） Fragment：JmjC Domain (UNP Residues 183-416)	Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；4.5% PEG 3000, 0.1 M Bis-Tris pH 5.5, 0.05 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.25 Å R-free 0.161
4GJZ JMJD5 in complex with 2-oxoglutarate Deposited 2012-08-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa） Fragment：JmjC Domain (UNP Residues 183-416)	Not recorded	CO COBALT (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；9.5% PEG 3000, 0.1 M Bis-Tris pH 6.2, 0.05 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.05 Å R-free 0.163
4QU1 Crystal structure of human JMJD5 jmj-c domain Deposited 2014-07-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa） Fragment：jmj-c domain (UNP residues 183-416)	Not recorded	NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 8% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.57 Å R-free 0.174
5FBJ Complex structure of JMJD5 and substrate Deposited 2015-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 NMM (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；281 K；PEG3350 HEPEPS-Na	Resolution 2.42 Å R-free 0.246
6AVS Complex structure of JMJD5 and Symmetric Monomethyl-Arginine (MMA) Deposited 2017-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 221–454（234 aa）	Not recorded	ZN ZINC ION × 1 NMM (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M HEPES pH 7.0 8% PEG 3350	Resolution 2.02 Å R-free 0.272
6AX3 Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA) Deposited 2017-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 222–454（233 aa）	Not recorded	2MR N3, N4-DIMETHYLARGININE × 1 AKG 2-OXOGLUTARIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M HEPES pH 7.0 8% PEG 3350	Resolution 2.25 Å R-free 0.259
6F4M Human JMJD5 in its apo form. Deposited 2017-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 182–416（235 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M Bis-Tris pH 6.5, 22.5 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)	Resolution 1.71 Å R-free 0.186
6F4N Human JMJD5 in complex with MN and 2OG. Deposited 2017-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 153–416（264 aa）	Not recorded	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1 M Bis-Tris pH 6.0, 21.4 % PEG3350, 0.07 M MgCl2, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)	Resolution 2.54 Å R-free 0.230
6F4N Human JMJD5 in complex with MN and 2OG. Deposited 2017-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 153–416（264 aa）	Not recorded	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1 M Bis-Tris pH 6.0, 21.4 % PEG3350, 0.07 M MgCl2, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)	Resolution 2.54 Å R-free 0.230
6F4O Human JMJD5 in complex with Mn(II) and Succinate. Deposited 2017-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	MN MANGANESE (II) ION × 1 SIN SUCCINIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 2:1 ratio)	Resolution 1.28 Å R-free 0.174
6F4P Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) Deposited 2017-11-29	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 A 183–416（234 aa） Fragment：Catalytic domain, UNP residues 183-416	Not recorded	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1M Bis-Tris pH 6.0, 26.4 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)	Resolution 1.45 Å R-free 0.168
6F4Q Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2) Deposited 2017-11-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 221–454（234 aa）	Mutation：C217A, C232A, Q275C, C295A, C384A	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1M Bis-Tris pH 6.0, 19.3 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)	Resolution 1.12 Å R-free 0.153
6F4R Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3) Deposited 2017-11-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Mutation：C217A, C232A, C295A, N308C, C384A Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；0.1M Bis-Tris pH 5.8, 25 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)	Resolution 1.30 Å R-free 0.162
6F4S Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4) Deposited 2017-11-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 183–416（234 aa）	Mutation：C217A, C232A, N308C	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 29 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)	Resolution 1.46 Å R-free 0.152
6F4T Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5) Deposited 2017-11-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa） Fragment：Catalytic domain, UNP residues 183-416	Mutation：C217A, C232A, W414C Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 17.1 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)	Resolution 1.22 Å R-free 0.154
6I9L JmjC domain-containing protein 5 (JMJD5) in complex with Mn and pyridine-2,4-dicarboxylic acid (2,4-PDCA) Deposited 2018-11-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	MN MANGANESE (II) ION × 1 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M BIS-TRIS PH 6.5, 15.0 % PEG3350, 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, 2:1 RATIO)	Resolution 1.53 Å R-free 0.164
6I9M JmjC domain-containing protein 5 (JMJD5) in complex with Mn and R-2-hydroxyglutarate Deposited 2018-11-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	MN MANGANESE (II) ION × 1 2HG (2R)-2-hydroxypentanedioic acid × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2	Resolution 1.65 Å R-free 0.181
6I9N JmjC domain-containing protein 5 (JMJD5) in complex with Mn and L-2-hydroxyglutarate Deposited 2018-11-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	MN MANGANESE (II) ION × 1 S2G (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2	Resolution 1.36 Å R-free 0.159
7DYT Human JMJD5 in complex with MN and 5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	MN MANGANESE (II) ION × 1 HR3 5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride	Resolution 1.62 Å R-free 0.189
7DYU Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MN MANGANESE (II) ION × 1 HR9 5-(4-phenylbutylamino)pyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride	Resolution 1.72 Å R-free 0.195
7DYW Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	HRL 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride	Resolution 2.13 Å R-free 0.239
7DYX Human JMJD5 in complex with MN and 5-((2-cyclopropylbenzyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	MN MANGANESE (II) ION × 1 HRR 5-((2-cyclopropylbenzyl)amino)pyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride	Resolution 2.27 Å R-free 0.280
7UQ3 JmjC domain-containing protein 5 (JMJD5) in complex with Mn and (S)-2-(1-hydroxy-2,5-dioxopyrrolidin-3-yl)acetic acid Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–416（234 aa）	Not recorded	MN MANGANESE (II) ION × 1 O2U [(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]acetic acid × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；Sample: 22 mg/mL JMJD5, 1.5 mM MnCl2, 5 mM compound (IS-52); Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2; Cryo-protection: 25% (v/v) glycerol; Method: 300 nL sitting drops (sample:well, 2:1 ratio)	Resolution 1.49 Å R-free 0.135

25 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDM8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–235； UniProt 183–416

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7dyv
Deposition date deposition_date	2021-01-23
Structure title title	Human JMJD5 in complex with MN and 5-(benzylamino)pyridine-2,4-dicarboxylic acid.
Keywords keywords	JmjC domain-containing protein 5, JMJD5, dioxygenase, 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	18.91 Å
Radius of gyration Rg (electron density) rg_electron	17.66 Å
Forward intensity I(0) i0	12001000.00
Molecular weight molecular_weight	26624.0 kDa
Excluded volume excluded_volume	33548 Å³
Envelope volume envelope_volume	37967 Å³
Hydration-shell volume shell_volume	17924 Å³
Envelope diameter envelope_diameter	59.9 Å
Shell Rg shell_rg	23.95 Å
Envelope Rg envelope_rg	17.99 Å
Shape Rg shape_rg	17.63 Å
Total Rg total_rg	18.70 Å
Total atoms total_atoms	3689
Residues n_residues	229
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	59.1 Å
Rg (real space) rg_real	18.81 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.2000e+07
I(0) uncertainty (real space) i0_real_error	1.2370e+05
Rg (reciprocal space) rg_reciprocal	18.82 Å
I(0) (reciprocal space) i0_reciprocal	12000000.0000
Solution quality estimate total_estimate	0.7558
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.431
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2461000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 0.374; Positv: 1.000; Valcen: 0.993; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Bifunctional peptidase and arginyl-hydroxylase JMJD5
Molecular weight formula_weight	27261.9 kDa
EC 编号 ec_number	1.14.11.-,3.4.-.-
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	4164

STVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS

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 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	5-(benzylamino)pyridine-2,4-dicarboxylic acid
Molecular weight formula_weight	272.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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8. Citations (1)

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Unit-cell length a length_a	49.338 Å
Unit-cell length b length_b	65.339 Å
Unit-cell length c length_c	78.610 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.920 Å
Low-resolution limit resolution_low	50.250 Å
R factor r_factor	0.2079
R_work r_work	0.2044
R_free r_free	0.2401

fit	/app/data/saxs_computation/dy/7dyv/7dyv.fit
pddf	/app/data/pr_computation/dy/7dyv/7dyv.pr.out
profile	/app/data/saxs_computation/dy/7dyv/7dyv.dat