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5lbb

HIF prolyl hydroxylase 2 (PHD2/EGLN1) R396T variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)

Method: X-RAY DIFFRACTION Dmax: 67.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Egl nine homolog 1

Homo sapiens

UniProt Q9GZT9

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 181–426 Fragment：CATALYTIC DOMAIN, UNP RESIDUES 181-426 Mutation：R396T MN MANGANESE (II) ION × 3 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 3 BCT BICARBONATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 2.1 M ammonium sulphate, 2% v/v dioxane, 0.002 M MnCl2 Resolution 1.70 Å R-free 0.178

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 5LBB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2G19 Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2) Deposited 2006-02-14 Different construct Different mutation/modification 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 181–418（238 aa） Fragment：CATALYTIC DOMAIN
Not recorded FE2 FE (II) ION × 1 4HG N-[(4-HYDROXY-8-IODOISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；298 K；28% polyethylene glycol 8000, 0.2 M ammonium sulfate, 100 mM MES buffer with 10 fold molar excess of inhibitor, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.40
Resolution 1.70 Å R-free 0.253
2G1M Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2) Deposited 2006-02-14 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN
Not recorded FE2 FE (II) ION × 1 4HG N-[(4-HYDROXY-8-IODOISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；1.6M AMMONIUM SULFATE, 4% DIOXANE, 0.1M MES PH6.5, ARGON ATMOSPHERE, 20MG/ML PROTEIN WITH 1MM FE(II)SO4, 2.0MM IIQ, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Resolution 2.20 Å R-free 0.289
2HBT Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor Deposited 2006-06-14 Different construct Different mutation/modification 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 188–426（239 aa） Fragment：catalytic domain
Not recorded FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；200-300 mM (NH4)2SO4, 100 mM NaOAc pH 4.8-5.4, 22-25% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.241
2HBU Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor Deposited 2006-06-14 Different construct Different mutation/modification 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 188–426（239 aa） Fragment：catalytic domain
Not recorded FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；200-300 mM (NH4)2SO4, 100 mM NaOAc pH 4.8-5.4, 22-25% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.85 Å R-free 0.231
2Y33 S-nitrosylated PHD2 (GSNO soaked) in complex with Zn(II) and UN9 Deposited 2010-12-18 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；APPROX. 20 MG/ML APO-PHD2, 1MM ZN-ACETATE, 1MM FG2, VAPOR DIFFUSION, SITTING DROP, 30% PEG 4000 (W/V), 0.2M SODIUM ACETATE, 0.1 M TRIS-HCL PH 8.5; PRE-GROWN CRYSTALS WERE SOAKED WITH 50 MM GSNO FOR 12 HR.
Resolution 2.00 Å R-free 0.246
2Y34 S-nitrosylated PHD2 (NO exposed) in complex with Fe(II) and UN9 Deposited 2010-12-18 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Non-standard monomer：Yes (specific site not provided by mmCIF) FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；1.6M AMMONIUM SULFATE, 4% DIOXANE, 0.1M MES PH6.5, VAPOR DIFFUSION, HANGING DROP, PRE-GROWN CRYSTALS WERE EXPOSED TO NITRIC OXIDE SATURATED SOLUTION (1 ML, DENSITY 1.34 G/L) FOR AN HOUR.
Resolution 2.01 Å R-free 0.225
3HQR PHD2:Mn:NOG:HIF1-alpha substrate complex Deposited 2009-06-08 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 181–426（246 aa） Fragment：PHD2 catalytic domain, residues 181-426
Mutation：R398A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.5；298 K；20% PEG 3350, 200mM MgCl2, pH 7.5, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.248
3HQU PHD2:Fe:UN9:partial HIF1-alpha substrate complex Deposited 2009-06-08 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 181–426（246 aa） Fragment：PHD2 catalytic domain, residues 181-426
Not recorded FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；1.6M AMMONIUM SULFATE, 4% DIOXANE, 0.1M MES PH6.5, ARGON ATMOSPHERE, 20MG/ML PROTEIN WITH 1MM FE(II)SO4, 10MM HIF1A-CODD-OH PEPTIDE, hanging drop, temperature 298K
Resolution 2.30 Å R-free 0.222
3OUH PHD2-R127 with JNJ41536014 Deposited 2010-09-14 Different construct Different mutation/modification 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 181–416（236 aa）
Not recorded FE2 FE (II) ION × 1 SO4 SULFATE ION × 1 014 1-(5-chloro-6-fluoro-1H-benzimidazol-2-yl)-1H-pyrazole-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2M AMMONIUM SULFATE/100MM IMIDAZOLE, 100 MM MAGNESIUM SULFATE/10% (V/V) GLYCEROL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.51 Å R-free 0.275
3OUI PHD2-R717 with 40787422 Deposited 2010-09-14 Different construct Different mutation/modification 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 181–392（212 aa）
Not recorded ACT ACETATE ION × 2 FE2 FE (II) ION × 1 42Z N-[(5,6-dichloro-1H-benzimidazol-2-yl)carbonyl]glycine × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.0 M AMMONIUM SULFATE, 2% PEG 400, 100 MM ACETATE, pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.217
3OUJ PHD2 with 2-Oxoglutarate Deposited 2010-09-14 Different construct Different mutation/modification 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 181–416（236 aa）
Not recorded SO4 SULFATE ION × 1 FE2 FE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.2 M AMMONIUM SULFATE, 28% PEG 8000, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.253
4BQW HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Mn(II) and 2-(4-hydroxy-2-oxo-1,2-dihydroquinoline-3-carboxamido)acetic acid Deposited 2013-06-03 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Not recorded MN MANGANESE (II) ION × 1 QNM 2-[(1-methyl-2-oxidanyl-4-oxidanylidene-quinolin-3-yl)carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES PH6.5, 1.7M AMMONIUM SULFATE, 1% DIOXANE, 0.002M MNCL2, SITTING DROP, 293K
Resolution 1.79 Å R-free 0.201
4BQX HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) Deposited 2013-06-03 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Not recorded MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES PH6.5, 1.7M AMMONIUM SULFATE, 1% DIOXANE, 0.002M MNCL2, SITTING DROP, 293K
Resolution 1.79 Å R-free 0.229
4BQY HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Fe(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]alanine Deposited 2013-06-03 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Not recorded FE2 FE (II) ION × 1 FNT (2S)-2-{[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]amino}propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1M MES PH6.5, 1.6M AMMONIUM SULFATE, 3% DIOXANE, 0.002M FECL2, NEAR ANAEROBIC
Resolution 1.53 Å R-free 0.228
4JZR Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors Deposited 2013-04-03 Different construct Different mutation/modification 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 189–399（211 aa） Fragment：UNP residues 189-399
Not recorded NI NICKEL (II) ION × 1 4JR 2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-2,8-diazaspiro[4.5]decan-1-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；30% PEG3350, 200mM Ammonium Sulfate, 100mM Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.259
4KBZ Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2) with (S)-{2-[2-(5-Cyano-3-hydroxy-pyridin-2-yl)-thiazol-4-yl]-acetylamino}-phenyl-acetic acid Deposited 2013-04-24 Different construct Different mutation/modification 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 184–419（236 aa） Fragment：Catalytic domain
Mutation：V410L 1QA (2S)-({[2-(5-cyano-3-hydroxypyridin-2-yl)-1,3-thiazol-4-yl]acetyl}amino)(phenyl)ethanoic acid × 1 FE2 FE (II) ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；0.1M HEPES, 35% PEG8K, 0.2M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.15 Å R-free 0.230
4UWD HIF prolyl hydroxylase 2 (PHD2/ EGLN1) D315E VARIANT in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) Deposited 2014-08-11 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Mutation：YES MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES PH6.5, 1.7M AMMONIUM SULFATE, 1% DIOXANE, 0.002M MNCL2, SITTING DROP, 293K
Resolution 1.72 Å R-free 0.173
5A3U HIF prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 6-(5-oxo-4-(1H- 1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid Deposited 2015-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Chain B 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Chain C 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Not recorded MN MANGANESE (II) ION × 6 R8J 6-(5-oxo-4-(1H-1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.6 M SODIUM CITRATE/CITRIC ACID PH 6.5, SITTING DROP, 293K
Resolution 3.30 Å R-free 0.227
5L9B HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-1ALPHA CODD (556-574) Deposited 2016-06-10 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 181–426（246 aa） Fragment：UNP residues 181-426
Mutation：C201A, R398A MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v polyethylene glycol 3350
Resolution 1.95 Å R-free 0.186
5L9B HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-1ALPHA CODD (556-574) Deposited 2016-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 181–426（246 aa） Fragment：UNP residues 181-426
Mutation：C201A, R398A MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v polyethylene glycol 3350
Resolution 1.95 Å R-free 0.186
5L9R HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) Deposited 2016-06-10 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 181-426
Mutation：C201A, R398A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 2 PG4 TETRAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES-Na pH 7.5, 2% v/v Polyethylene glycol 400, 2.0 M ammonium sulfate
Resolution 1.81 Å R-free 0.188
5L9V HIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-1) Deposited 2016-06-11 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 181–426（246 aa） Fragment：Catalytic domain, UNP RESIDUES 181-426
Mutation：C201A, R281C, P317C, R398A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium chloride, 20 % w/v polyethylene glycol 3350
Resolution 1.83 Å R-free 0.190
5L9V HIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-1) Deposited 2016-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 181–426（246 aa） Fragment：Catalytic domain, UNP RESIDUES 181-426
Mutation：C201A, R281C, P317C, R398A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium chloride, 20 % w/v polyethylene glycol 3350
Resolution 1.83 Å R-free 0.190
5LA9 HIF prolyl hydroxylase 2 (PHD2-R281C/V314C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-2) Deposited 2016-06-14 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN UNP residues 181-426
Mutation：C201A, R281C, V314C, R398A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate
Resolution 2.81 Å R-free 0.279
5LA9 HIF prolyl hydroxylase 2 (PHD2-R281C/V314C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-2) Deposited 2016-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 181–426（246 aa） Fragment：CATALYTIC DOMAIN UNP residues 181-426
Mutation：C201A, R281C, V314C, R398A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate
Resolution 2.81 Å R-free 0.279
5LAS HIF prolyl hydroxylase 2 (PHD2-R281C/P317C/R396T) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-3) Deposited 2016-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 181–426（246 aa） Fragment：CATALYTIC DOMAIN, UNP residues 181-426
Chain B 181–426（246 aa） Fragment：CATALYTIC DOMAIN, UNP residues 181-426
Mutation：C201A, R281C, P317C, R396T, R398A Mutation：C201A, R281C, P317C, R396T, R398A MN MANGANESE (II) ION × 2 OGA N-OXALYLGLYCINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1 M citrate pH 5.0, 20 % w/v polyethylene glycol 6000
Resolution 2.10 Å R-free 0.221
5LAT HIF prolyl hydroxylase 2 (PHD2/EGLN1) P317R variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) Deposited 2016-06-15 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, UNP residues 181-426
Mutation：P317R MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 GOL GLYCEROL × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M tri-sodium citrate pH 5.6, 20% PEG 4000, 20% 2-propanol
Resolution 1.90 Å R-free 0.166
5LB6 HIF prolyl hydroxylase 2 (PHD2/EGLN1) R371H variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) Deposited 2016-06-15 Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, UNP RESIDUES 181-426
Mutation：R371H MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES-Na pH 6.5, 30% polyethylene glycol monomethyl ether 5000, 0.2 M ammonium sulphate
Resolution 1.70 Å R-free 0.168
5LBC HIF prolyl hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) Deposited 2016-06-15 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN (181-426)
Mutation：I280V, R281L, I292V MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 2 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.8 M ammonium sulphate, 5% v/v dioxane, 0.002 M MnCl2
Resolution 1.82 Å R-free 0.181
5LBE HIF prolyl hydroxylase 2 (PHD2/EGLN1) G294E variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) Deposited 2016-06-15 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN (181-426)
Mutation：G294E MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 2.0 M ammonium sulphate, 7% v/v dioxane, 0.002 M MnCl2
Resolution 1.75 Å R-free 0.177
5LBF HIF prolyl hydroxylase 2 (PHD2/EGLN1) K293K/G294E variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) Deposited 2016-06-16 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN (181-426)
Mutation：K293K, G294E MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 SO4 SULFATE ION × 2 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.8 M ammonium sulphate, 2% v/v dioxane, 0.002 M MnCl2
Resolution 1.90 Å R-free 0.185
5OX5 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with CCT6, a GSK1278863-related compound Deposited 2017-09-06 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, UNP residues 181-426
Not recorded MN MANGANESE (II) ION × 1 B2E (6-hydroxy-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbonyl)glycine × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.5 M sodium citrate tribasic dehydrate pH 6.5, Sitting drop (300 nl), protein-to-well ratio, 1:1.
Resolution 2.25 Å R-free 0.205
5OX6 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Vadadustat Deposited 2017-09-06 Different construct Different mutation/modification 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 181–426（246 aa） Fragment：CATALYTIC DOMAIN, UNP residues 181-426
Not recorded MN MANGANESE (II) ION × 1 A1Z Vadadustat × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4000, Sitting drop (300 nl), protein-to-well ratio, 2:1
Resolution 1.99 Å R-free 0.205
5V18 Structure of PHD2 in complex with 1,2,4-Triazolo-[1,5-a]pyridine Deposited 2017-03-01 Different construct Different mutation/modification 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 80–315（236 aa） Fragment：UNP residues 80-315
Not recorded SO4 SULFATE ION × 2 8UY 4-([1,2,4]triazolo[1,5-a]pyridin-5-yl)benzonitrile × 1 FE2 FE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 335, 200 mM ASO4, 100 mM Bis-Tris pH 6.5
Resolution 2.15 Å R-free 0.235
6NMQ Hypoxia-Inducible Factor (HIF) Prolyl Hydroxylase 2 (PHD2) in Complex with the Carboxamide Analog JNJ43058171 Deposited 2019-01-11 Different construct Different mutation/modification 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 180–392（213 aa） Fragment：UNP Residues 180-392
Not recorded FE2 FE (II) ION × 1 KU1 N-(4-oxo-1,4-dihydrocinnoline-3-carbonyl)glycine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M AMMONIUM SULFATE/100MM IMIDAZOLE, 100 MM MAGNESIUM SULFATE/10% (V/V) GLYCEROL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.58 Å R-free 0.260
6QGV HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with a Spiro[4.5]decanone inhibitor (JPHM-2-167) Deposited 2019-01-13 Different construct Different mutation/modification 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 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 J2H 8-[(3-methylpyridin-2-yl)methyl]-3-(4-phenylphenyl)-1-pyrimidin-2-yl-1,3,8-triazaspiro[4.5]decane-2,4-dione × 1 GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.0 M Ammonium sulfate, 5% v/v 2-propanol
Resolution 1.40 Å R-free 0.172
6ST3 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide Deposited 2019-09-10 Different construct Different mutation/modification 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 181–407（227 aa）
Not recorded LUW 4-oxidanyl-~{N}-[(4-phenoxyphenyl)methyl]-2-pyrazol-1-yl-pyrimidine-5-carboxamide × 1 FMT FORMIC ACID × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% PEG 4000, Sitting drop (300 nl), protein-to-well ratio, 1:2, 293K
Resolution 2.43 Å R-free 0.217
6ST3 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide Deposited 2019-09-10 Different construct Different mutation/modification 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 181–407（227 aa）
Not recorded LUW 4-oxidanyl-~{N}-[(4-phenoxyphenyl)methyl]-2-pyrazol-1-yl-pyrimidine-5-carboxamide × 1 FMT FORMIC ACID × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% PEG 4000, Sitting drop (300 nl), protein-to-well ratio, 1:2, 293K
Resolution 2.43 Å R-free 0.217
6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 Deposited 2020-04-28 Different construct Different mutation/modification 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 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 PW2 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.
Resolution 2.85 Å R-free 0.266
6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 Deposited 2020-04-28 Different construct Different mutation/modification 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 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 PW2 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.
Resolution 2.85 Å R-free 0.266
6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 Deposited 2020-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 PW2 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.
Resolution 2.85 Å R-free 0.266
6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 Deposited 2020-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 PW2 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.
Resolution 2.85 Å R-free 0.266
6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 Deposited 2020-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 PW2 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.
Resolution 2.85 Å R-free 0.266
6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 Deposited 2020-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 PW2 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.
Resolution 2.85 Å R-free 0.266
6YVW HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with monocyclic BB-328 Deposited 2020-04-28 Different construct Different mutation/modification 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 181–426（246 aa）
Not recorded FE FE (III) ION × 1 PW5 4-[(5-bromanyl-4,6-dimethyl-pyridin-2-yl)amino]-4-oxidanylidene-butanoic acid × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sample: (20 mg/ml PHD2 + 1 mM FeSO4 + 2 mM compound); Reservoir: 1.6-2.0 M (NH4)2SO4, 2-8% dioxane, 0.1 M MES-Na pH 6.5, and 1 mM FeSO4; Hanging drop (2 ul), protein-to-well ratio, 1:1, 293K
Resolution 1.97 Å R-free 0.208
6YVX HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic BB-287 Deposited 2020-04-28 Different construct Different mutation/modification 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 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 2JP 4-(isoquinolin-3-ylamino)-4-oxobutanoic acid × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sample: (20 mg/ml PHD2 + 1 mM FeSO4 + 2 mM compound); Reservoir: 1.6-2.0 M (NH4)2SO4, 2-8% dioxane, 0.1 M MES-Na pH 6.5, and 1 mM FeSO4; hanging drop vapour diffusion
Resolution 1.80 Å R-free 0.189
6YVZ HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic JLS-367 Deposited 2020-04-29 Different construct Different mutation/modification 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 181–426（246 aa）
Not recorded MN MANGANESE (II) ION × 1 PW8 4-[(5-bromanylisoquinolin-3-yl)amino]-4-oxidanylidene-butanoic acid × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: (~20 mg/ml-1 PHD2 + 1 mM MnCl2 + 2 mM compound); Reservoir: 1.6-2.0 M (NH4)2SO4, 2-8% dioxane, 0.1 M MES-Na pH 6.5, and 1 mM MnCl2; Sitting drop (2 ul), protein-to-well ratio, 1:1, 293K
Resolution 1.91 Å R-free 0.203
6YW0 Lysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with BB-287 Deposited 2020-04-29 Different construct Different mutation/modification 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 181–426（246 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FE FE (III) ION × 1 2JP 4-(isoquinolin-3-ylamino)-4-oxobutanoic acid × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Sample: 18 mg/mL PHD2-Me + 1 mM FeSO4 + 2 mM compound; Reservoir: 1.7% polyethylene glycol 400, 15% glycerol, 1.7 M ammonium sulphate and 0.085 M HEPES-Na pH 7.5; Sitting drop (2 uL), protein-to-well ratio, 1:1
Resolution 2.20 Å R-free 0.221
6YW1 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent allosteric cyclic peptide 3C (14-mer) Deposited 2020-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Sample: 1.0 mM PHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG 3350, 0.002 M MnCl2; Sitting drop (300 nl), protein-to-well ratio, 1:2
Resolution 1.46 Å R-free 0.175
6YW2 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic FG2216 and RaPID-derived cyclic peptide 3C (14-mer) Deposited 2020-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Sample: 1.0 mM PHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 22% w/v polyethylene glycol 3350, 0.25 M magnesium formate, 2 mM MnCl2; Sitting drop (2 ul), protein-to-well ratio, 1:1
Resolution 2.14 Å R-free 0.196
6YW3 HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl Glycine (NOG), HIF-1ALPHA CODD (556-574) and a RaPID-derived cyclic peptide 3C (14-mer) Deposited 2020-04-29 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 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C, 2.0 mM CODD; Reservoir: 19-23% w/v polyethylene glycol 3350, 0.25 M lithium sulfate, 2 mM MnCl2; Sitting drop (2 ul), protein-to-well ratio, 1:1
Resolution 2.28 Å R-free 0.208
6YW4 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer) Deposited 2020-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 181–407（227 aa）
Mutation：C201A/R398A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 8.5, 1.26 M ammonium sulfate; Sitting drop (300 nl), protein-to-well ratio, 1:1
Resolution 1.53 Å R-free 0.177
6ZBN HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4) Deposited 2020-06-08 Different construct Different mutation/modification 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 181–407（227 aa）
Not recorded QEE ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl)pyrazol-1-yl]pyridine-3-carboxylate × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Resolution 2.01 Å R-free 0.230
6ZBN HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4) Deposited 2020-06-08 Different construct Different mutation/modification 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 181–407（227 aa）
Not recorded QEE ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl)pyrazol-1-yl]pyridine-3-carboxylate × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Resolution 2.01 Å R-free 0.230
6ZBN HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 181–407（227 aa）
Not recorded QEE ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl)pyrazol-1-yl]pyridine-3-carboxylate × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Resolution 2.01 Å R-free 0.230
6ZBN HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 181–407（227 aa）
Not recorded QEE ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl)pyrazol-1-yl]pyridine-3-carboxylate × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Resolution 2.01 Å R-free 0.230
6ZBN HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 181–407（227 aa）
Not recorded QEE ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl)pyrazol-1-yl]pyridine-3-carboxylate × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Resolution 2.01 Å R-free 0.230
6ZBN HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 181–407（227 aa）
Not recorded QEE ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl)pyrazol-1-yl]pyridine-3-carboxylate × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Resolution 2.01 Å R-free 0.230
6ZBO HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-5-ol (Molidustat) Deposited 2020-06-08 Different construct Different mutation/modification 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 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 QEQ 2-(6-morpholin-4-ylpyrimidin-4-yl)-4-(1,2,3-triazol-1-yl)pyrazol-3-ol × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Potassium thiocyanate pH 7, 21% PEG 3350, Sitting drop (300 nL), protein-to-well ratio 2:1, 298K
Resolution 1.79 Å R-free 0.206
6ZBO HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-5-ol (Molidustat) Deposited 2020-06-08 Different construct Different mutation/modification 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 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 QEQ 2-(6-morpholin-4-ylpyrimidin-4-yl)-4-(1,2,3-triazol-1-yl)pyrazol-3-ol × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Potassium thiocyanate pH 7, 21% PEG 3350, Sitting drop (300 nL), protein-to-well ratio 2:1, 298K
Resolution 1.79 Å R-free 0.206
6ZBO HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-5-ol (Molidustat) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 QEQ 2-(6-morpholin-4-ylpyrimidin-4-yl)-4-(1,2,3-triazol-1-yl)pyrazol-3-ol × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Potassium thiocyanate pH 7, 21% PEG 3350, Sitting drop (300 nL), protein-to-well ratio 2:1, 298K
Resolution 1.79 Å R-free 0.206
6ZBO HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-5-ol (Molidustat) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 QEQ 2-(6-morpholin-4-ylpyrimidin-4-yl)-4-(1,2,3-triazol-1-yl)pyrazol-3-ol × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Potassium thiocyanate pH 7, 21% PEG 3350, Sitting drop (300 nL), protein-to-well ratio 2:1, 298K
Resolution 1.79 Å R-free 0.206
6ZBO HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-5-ol (Molidustat) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 QEQ 2-(6-morpholin-4-ylpyrimidin-4-yl)-4-(1,2,3-triazol-1-yl)pyrazol-3-ol × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Potassium thiocyanate pH 7, 21% PEG 3350, Sitting drop (300 nL), protein-to-well ratio 2:1, 298K
Resolution 1.79 Å R-free 0.206
6ZBO HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-5-ol (Molidustat) Deposited 2020-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 QEQ 2-(6-morpholin-4-ylpyrimidin-4-yl)-4-(1,2,3-triazol-1-yl)pyrazol-3-ol × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Potassium thiocyanate pH 7, 21% PEG 3350, Sitting drop (300 nL), protein-to-well ratio 2:1, 298K
Resolution 1.79 Å R-free 0.206
7Q5V HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542) Deposited 2021-11-04 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 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 PEG DI(HYDROXYETHYL)ETHER × 3 GOL GLYCEROL × 1 FMT FORMIC ACID × 3 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM NOG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.31 M Magnesium formate (range: 0.25-0.39 M), 16.6% w/v polyethylene glycol 3350 (range: 18-22%); Sitting drop (200 nl): protein-to-well ratio, 1:1; Cryo-protectant: 15% v/v dilution of reservoir with glycerol
Resolution 1.17 Å R-free 0.179
7Q5X HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542) Deposited 2021-11-04 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 181–407（227 aa）
Not recorded MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 FMT FORMIC ACID × 11 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM 2OG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.33 M Magnesium formate (range: 0.25-0.39 M), 17.5% w/v polyethylene glycol 3350 (range: 18-22%); Sitting drop (200 nl): protein-to-well ratio, 1:1; Cryo-protectant: 15% v/v dilution of reservior solution with glycerol
Resolution 1.21 Å R-free 0.176
7UJV Structure of PHD2 in complex with HIF2a-CODD Deposited 2022-03-31 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 B 181–426（246 aa）
Not recorded OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；32.5% (w/v) PEG 2000 MME
Resolution 1.80 Å R-free 0.213
7UMP CRYSTAL STRUCTURE OF PHD2 CATALYTIC DOMAIN (CID 7465) IN COMPLEX WITH AKB-6548 AT 1.8 A RESOLUTION Deposited 2022-04-07 Different construct Different mutation/modification 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 188–403（216 aa）
Not recorded FE2 FE (II) ION × 1 A1Z Vadadustat × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；299 K；100 MM SODIUM ACETATE PH 5.5, 21% PEG1500, 15% MPD, 300 MM MGSO4, 4 MM AKB-6548
Resolution 1.80 Å R-free 0.202
8J1K co-crystal structure of non-carboxylic acid inhibitor with PHD2 Deposited 2023-04-13 Different construct Different mutation/modification 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 189–406（218 aa）
Not recorded SY6 N-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3R)-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M NH4 phosphate monobasic,0.1M Tris,8.5,50% MPD
Resolution 2.45 Å R-free 0.308
8Q5S Anaerobic crystal structure of apo-HIF prolyl hydroxylase 2 (PHD2 181-407)in complex with acetate (ACT) and HIF2alpha-CODD peptide Deposited 2023-08-09 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 181–407（227 aa）
Not recorded ACT ACETATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(10-35%) PEG 4K, 0.2 M ammonium acetate, 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)
Resolution 1.49 Å R-free 0.213
8Q64 Crystal structure of hydroxylated HIF2alpha-CODD peptide (523-542) bound to apo-HIF prolyl hydroxylase 2 (PHD2 181-407) Deposited 2023-08-10 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 181–407（227 aa）
Not recorded ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；10-35% PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)
Resolution 1.36 Å R-free 0.212
8Q6D Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with HIF2alpha-CODD peptide (523-542), Fe(II) and 2-oxoglutarate (2OG) Deposited 2023-08-11 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 181–407（227 aa）
Not recorded FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；10-35% PEG 4K, 0.2 ammonium acetate, sodium ammonium acetate trihydrate pH (4.1-5.6)
Resolution 1.40 Å R-free 0.190
8Q6E Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with Fe(III), 2-oxoglutarate (2OG) and HIF2alpha-CODD peptide Deposited 2023-08-11 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 181–407（227 aa）
Not recorded MG MAGNESIUM ION × 3 CL CHLORIDE ION × 2 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(10-35%) PEG 4K, 0.2 M ammonium acetate , 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)
Resolution 1.37 Å R-free 0.205
8RUT HIF prolyl-hydroxylase-2 (PHD2) T387V variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor-2alpha (HIF-2alpha) Deposited 2024-01-31 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 181–407（227 aa）
Not recorded ACT ACETATE ION × 1 AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).
Resolution 1.62 Å R-free 0.219
8RUV HIF prolyl hydroxylase 2 (PHD2) T387I variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor 2alpha (HIF2alpha) Deposited 2024-01-31 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 181–407（227 aa）
Not recorded FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).
Resolution 1.66 Å R-free 0.257
8RUZ Anaerobic HIF prolyl-hydroxylase-2 (PHD2) T387S variant bound to acetate (ACT) and Hypoxia-inducible Factor-2alpha (HIF-2alpha) Deposited 2024-01-31 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 181–407（227 aa）
Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).
Resolution 1.82 Å R-free 0.314
8RV1 HIF prolyl hydroxylase 2 (PHD2) T387S variant bound to acetate (ACT) and hydroxylated Hypoxia-inducible Factor 2alpha (HIF2alpha) Deposited 2024-01-31 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 181–407（227 aa）
Not recorded ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).
Resolution 1.39 Å R-free 0.191
8Y0V HIF prolyl hydroxylase 2 in complex with inhibitor Deposited 2024-01-23 Different construct Different mutation/modification 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 181–426（246 aa）
Not recorded A1D5X ~{tert}-butyl 4-[6-[(6-cyanopyridin-3-yl)methylcarbamoyl]-5-oxidanyl-1,7-naphthyridin-2-yl]piperazine-1-carboxylate × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Ammonium phosphate monobasic, 0.1M Tris (8.3 8.7), 40% MPD
Resolution 2.50 Å R-free 0.291
8Z31 Crystal Structure of HIF-PHD2 in complex with compound 1 Deposited 2024-04-14 Different construct Different mutation/modification 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 188–403（216 aa）
Not recorded FE2 FE (II) ION × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 A1L0U 2-[(2,6-dimethyl-5-oxidanyl-pyrimidin-4-yl)carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Protein (30mg/ml in a final buffer of 20mM Tril-HCl (pH 7.5), 50mM NaCl), Reservoir solution (30% (w/v) PEG MME 5000, 0.2M ammonium sulfate, 0.1M HEPES (pH 7.0))
Resolution 1.81 Å R-free 0.216
8Z32 Crystal Structure of HIF-PHD2 in complex with compound 3 Deposited 2024-04-14 Different construct Different mutation/modification 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 188–426（239 aa）
Not recorded FE2 FE (II) ION × 1 A1L0V 2-[[6-[(4-fluorophenyl)methyl]-2-methyl-5-oxidanyl-pyrimidin-4-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Protein (30mg/ml in 20mM Tril-HCl (pH 7.5), 50mM NaCl), reservoir solution (1.3M ammonium sulfate, 20mM reduced glutathione, 2mM oxidized glutathione, 0.08M HEPES (pH 7.5))
Resolution 2.50 Å R-free 0.245
8Z32 Crystal Structure of HIF-PHD2 in complex with compound 3 Deposited 2024-04-14 Different construct Different mutation/modification 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 188–426（239 aa）
Not recorded FE2 FE (II) ION × 1 A1L0V 2-[[6-[(4-fluorophenyl)methyl]-2-methyl-5-oxidanyl-pyrimidin-4-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Protein (30mg/ml in 20mM Tril-HCl (pH 7.5), 50mM NaCl), reservoir solution (1.3M ammonium sulfate, 20mM reduced glutathione, 2mM oxidized glutathione, 0.08M HEPES (pH 7.5))
Resolution 2.50 Å R-free 0.245
8Z33 Crystal Structure of HIF-PHD2 in complex with compound 4 Deposited 2024-04-14 Different construct Different mutation/modification 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 188–426（239 aa）
Not recorded FE2 FE (II) ION × 1 F FLUORIDE ION × 1 A1L0W 2-[[6-[2-(4-fluorophenyl)ethyl]-2-methyl-5-oxidanyl-pyrimidin-4-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Protein (30mg/ml in 20mM Tril-HCl (pH 7.5), 50mM NaCl), reservoir solution (1.3M ammonium sulfate, 0.1M NaCl, 0.05M NaF, 0.1M HEPES (pH 7.5))
Resolution 2.60 Å R-free 0.249
8Z33 Crystal Structure of HIF-PHD2 in complex with compound 4 Deposited 2024-04-14 Different construct Different mutation/modification 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 188–426（239 aa）
Not recorded FE2 FE (II) ION × 1 F FLUORIDE ION × 1 A1L0W 2-[[6-[2-(4-fluorophenyl)ethyl]-2-methyl-5-oxidanyl-pyrimidin-4-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Protein (30mg/ml in 20mM Tril-HCl (pH 7.5), 50mM NaCl), reservoir solution (1.3M ammonium sulfate, 0.1M NaCl, 0.05M NaF, 0.1M HEPES (pH 7.5))
Resolution 2.60 Å R-free 0.249
8Z35 Crystal Structure of HIF-PHD2 in complex with compound 7 (DS44470011) Deposited 2024-04-14 Different construct Different mutation/modification 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 188–403（216 aa）
Not recorded FE2 FE (II) ION × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 A1L0X 2-[[6-methyl-5-oxidanyl-2-[(4-phenylphenyl)methyl]pyrimidin-4-yl]carbonylamino]ethanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Protein (30mg/ml in 20mM Tril-HCl (pH 7.5), 50mM NaCl), reservoir solution (30% (w/v) PEG MME 5000, 0.2M ammonium sulfate, 0.1M HEPES (pH 7.0))
Resolution 2.00 Å R-free 0.216

63 other PDB entries and 84 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGLN1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–252； UniProt 181–426

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 5lbb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lbb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5lbb
Deposition date deposition_date2016-06-15
Structure title titleHIF prolyl hydroxylase 2 (PHD2/EGLN1) R396T variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)
Keywords keywords;OXIDOREDUCTASE, NON-HEME DIOXYGENASE, IRON, 2-OXOGLUTARATE, HYPOXIA-INDUCIBLE FACTOR, HIF, HIF PROLYL HYDROXYLASE DOMAIN 2, PHD2, EGLN1, OXYGENASE, HYPOXIA, DNA-BINDING, METAL-BINDING, TRANSCRIPTION, HELIX-LOOP-HELIX-BETA, DSBH, FACIAL TRIAD, CYTOPLASM, TRANSCRIPTION/EPIGENETIC REGULATION, SIGNALING, DEVELOPMENT, CELL STRUCTURE, BETA-HYDROXYLATION, TRANSCRIPTION ACTIVATOR/INHIBITOR, UBL CONJUGATION, POLYMORPHISM, VITAMIN C, ZINC-FINGER, FAMILIAL ERYTHROCYTOSIS, BREAST CANCER, TRANSCRIPTION COMPLEX ;; 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_guinier18.68 Å
Radius of gyration Rg (electron density) rg_electron17.70 Å
Forward intensity I(0) i011988500.00
Molecular weight molecular_weight25211.0 kDa
Excluded volume excluded_volume31224 ų
Envelope volume envelope_volume36860 ų
Hydration-shell volume shell_volume17515 ų
Envelope diameter envelope_diameter67.3 Å
Shell Rg shell_rg23.94 Å
Envelope Rg envelope_rg18.45 Å
Shape Rg shape_rg17.70 Å
Total Rg total_rg18.64 Å
Total atoms total_atoms3425
Residues n_residues229
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 dmax67.5 Å
Rg (real space) rg_real18.61 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real1.1990e+07
I(0) uncertainty (real space) i0_real_error1.4310e+05
Rg (reciprocal space) rg_reciprocal18.62 Å
I(0) (reciprocal space) i0_reciprocal11990000.0000
Solution quality estimate total_estimate0.8393
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1 Å
Skewness Skewness skewness0.249
Kurtosis Kurtosis kurtosis-0.189
Angular range angular_range— – 0.4250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2140000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.644; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5lbba_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.2 — Clavaminate synthase-like
Family Family familyb.82.2.15 — proly-4-hydroxylase (P4H, PHD) like

CATH v4.4 (1 domains)

Domain ID domain_id5lbbA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily620 — q2cbj1_9rhob like domain
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8. Citations (3)

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9. Files and Curves (10)