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4gaz

Crystal Structure of a Jumonji Domain-containing Protein JMJD5

Method: X-RAY DIFFRACTION Dmax: 100.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific demethylase 8

Homo sapiens

UniProt Q8N371

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 176–416 Fragment：JmjC domain, UNP residues 176-416 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 176–416 Fragment：JmjC domain, UNP residues 176-416 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

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 4GAZ 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
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 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）
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 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）
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 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）
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 construct 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 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）
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 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）
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 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）
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 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）
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 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）
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
7DYV Human JMJD5 in complex with MN and 5-(benzylamino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23 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）
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
7DYW Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23 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）
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 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）
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 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）
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 27 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 4–244； UniProt 176–416 Author chain B； PDBConstruct 4–244； UniProt 176–416

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

SAXS profile for 4gaz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gaz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gaz
Deposition date deposition_date2012-07-26
Structure title titleCrystal Structure of a Jumonji Domain-containing Protein JMJD5
Keywords keywordsJmjC domain, demethylase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.32 Å
Radius of gyration Rg (electron density) rg_electron29.94 Å
Forward intensity I(0) i046571200.00
Molecular weight molecular_weight54840.0 kDa
Excluded volume excluded_volume69044 ų
Envelope volume envelope_volume87717 ų
Hydration-shell volume shell_volume25798 ų
Envelope diameter envelope_diameter102.4 Å
Shell Rg shell_rg34.98 Å
Envelope Rg envelope_rg29.83 Å
Shape Rg shape_rg29.93 Å
Total Rg total_rg30.47 Å
Total atoms total_atoms3876
Residues n_residues470
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax100.7 Å
Rg (real space) rg_real30.57 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real4.6570e+07
I(0) uncertainty (real space) i0_real_error6.8250e+05
Rg (reciprocal space) rg_reciprocal30.47 Å
I(0) (reciprocal space) i0_reciprocal46570000.0000
Solution quality estimate total_estimate0.8149
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary25.2 Å
Skewness Skewness skewness0.461
Kurtosis Kurtosis kurtosis-0.606
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18880000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.672; Smooth: 0.798
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4gazA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4gazB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
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8. Citations (1)

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9. Files and Curves (10)