当前蛋白身份：Q9GZT9
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差异标签只比较当前检索结果；所有PDB和assembly原始记录仍分别保留。
相关结构差异明细
一行代表一个 PDB 条目中的一个 biological assembly；同一蛋白的多个单体会分别列出。
| PDB 条目 | Assembly / 聚集状态 | 构建体 | 突变与修饰 | 配体、离子与非聚合物 | 实验方法 | 实验环境 | 结构质量 |
|---|---|---|---|---|---|---|---|
| 2G19 Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2) 提交 2006-02-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–418（238 aa）
片段：CATALYTIC DOMAIN
|
未记录 | FE2 FE (II) ION × 1 4HG N-[(4-HYDROXY-8-IODOISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 1.70 Å R-free 0.253 |
| 2G1M Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2) 提交 2006-02-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN
|
未记录 | FE2 FE (II) ION × 1 4HG N-[(4-HYDROXY-8-IODOISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 2.20 Å R-free 0.289 |
| 2HBT Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor 提交 2006-06-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
188–426（239 aa）
片段：catalytic domain
|
未记录 | FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 1.60 Å R-free 0.241 |
| 2HBU Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor 提交 2006-06-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
188–426（239 aa）
片段：catalytic domain
|
未记录 | FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 1.85 Å R-free 0.231 |
| 2Y33 S-nitrosylated PHD2 (GSNO soaked) in complex with Zn(II) and UN9 提交 2010-12-18 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
非标准单体：是（mmCIF未提供具体位点） | ZN ZINC ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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.
|
分辨率 2.00 Å R-free 0.246 |
| 2Y34 S-nitrosylated PHD2 (NO exposed) in complex with Fe(II) and UN9 提交 2010-12-18 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
非标准单体：是（mmCIF未提供具体位点） | FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 2 | X-RAY DIFFRACTION |
X-ray结晶条件
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.
|
分辨率 2.01 Å R-free 0.225 |
| 3HQR PHD2:Mn:NOG:HIF1-alpha substrate complex 提交 2009-06-08 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：PHD2 catalytic domain, residues 181-426
|
突变：R398A | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
hanging drop；pH 7.5；298 K；20% PEG 3350, 200mM MgCl2, pH 7.5, hanging drop, temperature 298K
|
分辨率 2.00 Å R-free 0.248 |
| 3HQU PHD2:Fe:UN9:partial HIF1-alpha substrate complex 提交 2009-06-08 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：PHD2 catalytic domain, residues 181-426
|
未记录 | FE2 FE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 2.30 Å R-free 0.222 |
| 3OUH PHD2-R127 with JNJ41536014 提交 2010-09-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–416（236 aa）
|
未记录 | 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结晶条件
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
|
分辨率 2.51 Å R-free 0.275 |
| 3OUI PHD2-R717 with 40787422 提交 2010-09-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–392（212 aa）
|
未记录 | 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结晶条件
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
|
分辨率 1.70 Å R-free 0.217 |
| 3OUJ PHD2 with 2-Oxoglutarate 提交 2010-09-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–416（236 aa）
|
未记录 | SO4 SULFATE ION × 1 FE2 FE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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 提交 2013-06-03 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2013-06-03 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
未记录 | MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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 提交 2013-06-03 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
未记录 | FE2 FE (II) ION × 1 FNT (2S)-2-{[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]amino}propanoic acid × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
pH 6.5；0.1M MES PH6.5, 1.6M AMMONIUM SULFATE, 3% DIOXANE, 0.002M FECL2, NEAR ANAEROBIC
|
分辨率 1.53 Å R-free 0.228 |
| 4JZR Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors 提交 2013-04-03 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
189–399（211 aa）
片段：UNP residues 189-399
|
未记录 | 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结晶条件
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
|
分辨率 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 提交 2013-04-24 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
184–419（236 aa）
片段：Catalytic domain
|
突变：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结晶条件
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
|
分辨率 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) 提交 2014-08-11 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
突变：YES | MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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 提交 2015-06-03 | Assembly 1 蛋白同源多聚体 同源多聚体；蛋白 × 6 PDB 声明：hexameric（6） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
链 B
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
链 C
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
未记录 | 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结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.6 M SODIUM CITRATE/CITRIC ACID PH 6.5, SITTING DROP, 293K
|
分辨率 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) 提交 2016-06-10 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：UNP residues 181-426
|
突变：C201A, R398A | MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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) 提交 2016-06-10 | Assembly 2 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 B
181–426（246 aa）
片段：UNP residues 181-426
|
突变：C201A, R398A | MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 1.95 Å R-free 0.186 |
| 5L9R HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) 提交 2016-06-10 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, RESIDUES 181-426
|
突变：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结晶条件
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
|
分辨率 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) 提交 2016-06-11 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：Catalytic domain, UNP RESIDUES 181-426
|
突变：C201A, R281C, P317C, R398A | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium chloride, 20 % w/v polyethylene glycol 3350
|
分辨率 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) 提交 2016-06-11 | Assembly 2 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 B
181–426（246 aa）
片段：Catalytic domain, UNP RESIDUES 181-426
|
突变：C201A, R281C, P317C, R398A | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium chloride, 20 % w/v polyethylene glycol 3350
|
分辨率 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) 提交 2016-06-14 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN UNP residues 181-426
|
突变：C201A, R281C, V314C, R398A | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate
|
分辨率 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) 提交 2016-06-14 | Assembly 2 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 B
181–426（246 aa）
片段：CATALYTIC DOMAIN UNP residues 181-426
|
突变：C201A, R281C, V314C, R398A | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate
|
分辨率 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) 提交 2016-06-14 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 4 PDB 声明：tetrameric（4） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, UNP residues 181-426
链 B
181–426（246 aa）
片段：CATALYTIC DOMAIN, UNP residues 181-426
|
突变：C201A, R281C, P317C, R396T, R398A 突变：C201A, R281C, P317C, R396T, R398A | MN MANGANESE (II) ION × 2 OGA N-OXALYLGLYCINE × 2 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1 M citrate pH 5.0, 20 % w/v polyethylene glycol 6000
|
分辨率 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) 提交 2016-06-15 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, UNP residues 181-426
|
突变：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结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M tri-sodium citrate pH 5.6, 20% PEG 4000, 20% 2-propanol
|
分辨率 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) 提交 2016-06-15 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, UNP RESIDUES 181-426
|
突变：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结晶条件
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
|
分辨率 1.70 Å R-free 0.168 |
| 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) 提交 2016-06-15 | Assembly 1 蛋白同源多聚体 同源多聚体；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, UNP RESIDUES 181-426
|
突变：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结晶条件
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
|
分辨率 1.70 Å R-free 0.178 |
| 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) 提交 2016-06-15 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN (181-426)
|
突变：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结晶条件
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
|
分辨率 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) 提交 2016-06-15 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN (181-426)
|
突变：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结晶条件
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
|
分辨率 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) 提交 2016-06-16 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN (181-426)
|
突变：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结晶条件
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
|
分辨率 1.90 Å R-free 0.185 |
| 5OX5 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with CCT6, a GSK1278863-related compound 提交 2017-09-06 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, UNP residues 181-426
|
未记录 | 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结晶条件
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.
|
分辨率 2.25 Å R-free 0.205 |
| 5OX6 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Vadadustat 提交 2017-09-06 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
片段：CATALYTIC DOMAIN, UNP residues 181-426
|
未记录 | MN MANGANESE (II) ION × 1 A1Z Vadadustat × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 1.99 Å R-free 0.205 |
| 5V18 Structure of PHD2 in complex with 1,2,4-Triazolo-[1,5-a]pyridine 提交 2017-03-01 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
80–315（236 aa）
片段：UNP residues 80-315
|
未记录 | 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结晶条件
VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 335, 200 mM ASO4, 100 mM Bis-Tris pH 6.5
|
分辨率 2.15 Å R-free 0.235 |
| 6NMQ Hypoxia-Inducible Factor (HIF) Prolyl Hydroxylase 2 (PHD2) in Complex with the Carboxamide Analog JNJ43058171 提交 2019-01-11 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
180–392（213 aa）
片段：UNP Residues 180-392
|
未记录 | FE2 FE (II) ION × 1 KU1 N-(4-oxo-1,4-dihydrocinnoline-3-carbonyl)glycine × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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) 提交 2019-01-13 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | 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结晶条件
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.0 M Ammonium sulfate, 5% v/v 2-propanol
|
分辨率 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 提交 2019-09-10 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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 提交 2019-09-10 | Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 B
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 2.43 Å R-free 0.217 |
| 6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 提交 2020-04-28 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
|
未记录 | 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结晶条件
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.
|
分辨率 2.85 Å R-free 0.266 |
| 6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 提交 2020-04-28 | Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 B
181–426（246 aa）
|
未记录 | 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结晶条件
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.
|
分辨率 2.85 Å R-free 0.266 |
| 6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 提交 2020-04-28 | Assembly 3 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 C
181–426（246 aa）
|
未记录 | 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结晶条件
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.
|
分辨率 2.85 Å R-free 0.266 |
| 6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 提交 2020-04-28 | Assembly 4 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 D
181–426（246 aa）
|
未记录 | 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结晶条件
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.
|
分辨率 2.85 Å R-free 0.266 |
| 6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 提交 2020-04-28 | Assembly 5 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 E
181–426（246 aa）
|
未记录 | 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结晶条件
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.
|
分辨率 2.85 Å R-free 0.266 |
| 6YVT HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 提交 2020-04-28 | Assembly 6 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 F
181–426（246 aa）
|
未记录 | 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结晶条件
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.
|
分辨率 2.85 Å R-free 0.266 |
| 6YVW HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with monocyclic BB-328 提交 2020-04-28 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
|
未记录 | 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结晶条件
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
|
分辨率 1.97 Å R-free 0.208 |
| 6YVX HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic BB-287 提交 2020-04-28 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
|
未记录 | MN MANGANESE (II) ION × 1 2JP 4-(isoquinolin-3-ylamino)-4-oxobutanoic acid × 1 BCT BICARBONATE ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 1.80 Å R-free 0.189 |
| 6YVZ HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic JLS-367 提交 2020-04-29 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
|
未记录 | 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结晶条件
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
|
分辨率 1.91 Å R-free 0.203 |
| 6YW0 Lysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with BB-287 提交 2020-04-29 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
|
非标准单体：是（mmCIF未提供具体位点） | FE FE (III) ION × 1 2JP 4-(isoquinolin-3-ylamino)-4-oxobutanoic acid × 1 BCT BICARBONATE ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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) 提交 2020-04-29 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 BCT BICARBONATE ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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) 提交 2020-04-29 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | MN MANGANESE (II) ION × 1 UN9 N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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) 提交 2020-04-29 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 3 PDB 声明：trimeric（3） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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) 提交 2020-04-29 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
突变：C201A/R398A | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 B
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 3 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 C
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 4 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 D
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 5 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 E
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 6 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 F
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 B
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 3 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 C
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 4 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 D
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 5 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 E
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2020-06-08 | Assembly 6 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 F
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2021-11-04 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 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) 提交 2021-11-04 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | 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结晶条件
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
|
分辨率 1.21 Å R-free 0.176 |
| 7UJV Structure of PHD2 in complex with HIF2a-CODD 提交 2022-03-31 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 B
181–426（246 aa）
|
未记录 | OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 FE FE (III) ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；32.5% (w/v) PEG 2000 MME
|
分辨率 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 提交 2022-04-07 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
188–403（216 aa）
|
未记录 | FE2 FE (II) ION × 1 A1Z Vadadustat × 1 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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
|
分辨率 1.80 Å R-free 0.202 |
| 8J1K co-crystal structure of non-carboxylic acid inhibitor with PHD2 提交 2023-04-13 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
189–406（218 aa）
|
未记录 | 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结晶条件
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M NH4 phosphate monobasic,0.1M Tris,8.5,50% MPD
|
分辨率 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 提交 2023-08-09 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | ACT ACETATE ION × 3 | X-RAY DIFFRACTION |
X-ray结晶条件
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)
|
分辨率 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) 提交 2023-08-10 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | ACT ACETATE ION × 4 | X-RAY DIFFRACTION |
X-ray结晶条件
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)
|
分辨率 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) 提交 2023-08-11 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, SITTING DROP；298 K；10-35% PEG 4K, 0.2 ammonium acetate, sodium ammonium acetate trihydrate pH (4.1-5.6)
|
分辨率 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 提交 2023-08-11 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | MG MAGNESIUM ION × 3 CL CHLORIDE ION × 2 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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)
|
分辨率 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) 提交 2024-01-31 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | ACT ACETATE ION × 1 AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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).
|
分辨率 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) 提交 2024-01-31 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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).
|
分辨率 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) 提交 2024-01-31 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | ACT ACETATE ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
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).
|
分辨率 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) 提交 2024-01-31 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric（2） 与蛋白数一致 |
链 A
181–407（227 aa）
|
未记录 | ACT ACETATE ION × 2 | X-RAY DIFFRACTION |
X-ray结晶条件
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).
|
分辨率 1.39 Å R-free 0.191 |
| 8Y0V HIF prolyl hydroxylase 2 in complex with inhibitor 提交 2024-01-23 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
181–426（246 aa）
|
未记录 | 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结晶条件
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Ammonium phosphate monobasic, 0.1M Tris (8.3 8.7),
40% MPD
|
分辨率 2.50 Å R-free 0.291 |
| 8Z31 Crystal Structure of HIF-PHD2 in complex with compound 1 提交 2024-04-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
188–403（216 aa）
|
未记录 | 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结晶条件
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))
|
分辨率 1.81 Å R-free 0.216 |
| 8Z32 Crystal Structure of HIF-PHD2 in complex with compound 3 提交 2024-04-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
188–426（239 aa）
|
未记录 | 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结晶条件
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))
|
分辨率 2.50 Å R-free 0.245 |
| 8Z32 Crystal Structure of HIF-PHD2 in complex with compound 3 提交 2024-04-14 | Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 B
188–426（239 aa）
|
未记录 | 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结晶条件
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))
|
分辨率 2.50 Å R-free 0.245 |
| 8Z33 Crystal Structure of HIF-PHD2 in complex with compound 4 提交 2024-04-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
188–426（239 aa）
|
未记录 | 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结晶条件
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))
|
分辨率 2.60 Å R-free 0.249 |
| 8Z33 Crystal Structure of HIF-PHD2 in complex with compound 4 提交 2024-04-14 | Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 B
188–426（239 aa）
|
未记录 | 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结晶条件
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))
|
分辨率 2.60 Å R-free 0.249 |
| 8Z35 Crystal Structure of HIF-PHD2 in complex with compound 7 (DS44470011) 提交 2024-04-14 | Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric（1） 与蛋白数一致 |
链 A
188–403（216 aa）
|
未记录 | 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结晶条件
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))
|
分辨率 2.00 Å R-free 0.216 |