6yyv

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 3-methyl-2-oxoglutarate

Method: X-RAY DIFFRACTION D_max: 90.1 Å Quality: GOOD

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Aspartyl/asparaginyl beta-hydroxylase

Homo sapiens

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 330–758	未记录	MN MANGANESE (II) ION × 1 Q1Z (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；200 mM magnesium acetate tetrahydrate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 3-methyl-2-oxoglutarate, 18 mg/ml protein	分辨率 1.77 Å R-free 0.208

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 6YYV	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
5APA Crystal structure of human aspartate beta-hydroxylase isoform a 提交 2015-09-15	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 562–758（197 aa）片段：UNP RESIDUES 562-758	未记录	NI NICKEL (II) ION × 1 LMR (2S)-2-hydroxybutanedioic acid × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 50MM SODIUM MALATE, 20% PEG3350, 3% DEXTRAN SULFATE, 20MM NISO4	分辨率 2.05 Å R-free 0.185
5JQY Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and factor X substrate peptide fragment(39mer-4Ser) 提交 2016-05-05	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）片段：UNP residues 330-758	未记录	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；100mM SPG buffer, 25% PEG 1500, 2mM NOG, 1mM MnCl2, 18mg/ml protein	分辨率 1.99 Å R-free 0.205
5JTC Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, 2,4-pyridine dicarboxylate and factor X substrate peptide fragment(39mer-4Ser) 提交 2016-05-09	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）片段：UNP Residues 330-758	未记录	MN MANGANESE (II) ION × 1 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 1 BR BROMIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20% PEG3350, 200mM NaBr, 100mM BisTris Propane, 1mM MnCl2, 2mM 2,4-PDCA, 330uM ASPH, 726uM Factor X	分辨率 2.24 Å R-free 0.208
5JZ6 Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese and L-malate 提交 2016-05-16	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 GOL GLYCEROL × 4 LMR (2S)-2-hydroxybutanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；1mM MMT buffer (DL-Malic acid, MES, Tris base), 25% PEG1500, 1 mM MnCl2, 2 mM N-oxalylglycine, 18 mg/ml protein	分辨率 2.35 Å R-free 0.220
5JZ8 Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine, and factor X substrate peptide fragment (39mer) 提交 2016-05-16	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis-tris propane, 200mM sodium acetate, 20% PEG 3350, 1 mM manganese chloride, 2 mM N-oxalylglycine, 726 uM FX peptide, 18 mg/ml protein	分辨率 2.10 Å R-free 0.216
5JZA Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese and N-oxalylglycine 提交 2016-05-16	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 GOL GLYCEROL × 4 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；100 mM bicine, 100 mM sodium chloride, 27% PEG 550 MME, 1 mM manganese chloride, 2 mM N-oxalylglycine, 18 mg/ml protein	分辨率 2.14 Å R-free 0.198
5JZU Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and factor X substrate peptide fragment (26mer) 提交 2016-05-17	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis-tris propane, 20 mM sodium/potassium phosphate, 20% PEG 3350, 1 mM manganese chloride, 2 mM N-oxalylglycine, 1.65 mM factor X peptide, 18 mg/ml asph protein	分辨率 2.50 Å R-free 0.229
6Q9F Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X peptide fragment (39mer-4Ser) 提交 2018-12-18	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	突变：H679A	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M sodium chloride 0.1 M Tris-HCl 8.0 20 % w/v PEG 6000	分辨率 1.63 Å R-free 0.200
6Q9I Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Factor X peptide fragment (39mer-4Ser) 提交 2018-12-18	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	突变：H679A	FMT FORMIC ACID × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium formate, 20 % w/v PEG 3350	分辨率 1.85 Å R-free 0.223
6QA5 Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in the apo form 提交 2018-12-18	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 301–729（429 aa）	突变：H679A	ACT ACETATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；0.1 M PCTP (Propionic acid, Cacodylate, Bis-tris propane) buffer pH 9.0 25 % w/v PEG 1500	分辨率 2.65 Å R-free 0.224
6RK9 Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and cyclic peptide substrate mimic of factor X 提交 2019-04-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis-tris propane, 200 mM potassium thiocyanate, 20% PEG 3350, 2 mM N-oxalylglycine, 1 mM manganese chloride, 3.3 mM cyclic peptide, 18 mg/ml asph protein	分辨率 2.29 Å R-free 0.235
6RK9 Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and cyclic peptide substrate mimic of factor X 提交 2019-04-30	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis-tris propane, 200 mM potassium thiocyanate, 20% PEG 3350, 2 mM N-oxalylglycine, 1 mM manganese chloride, 3.3 mM cyclic peptide, 18 mg/ml asph protein	分辨率 2.29 Å R-free 0.235
6YYU Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 2-oxoglutarate 提交 2020-05-06	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100 mM HEPES sodium, 10% v/v 2-Propanol, 20% w/v PEG 4000, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein	分辨率 2.11 Å R-free 0.231
6YYW Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) 提交 2020-05-06	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100 mM Bis Tris Propane, 200 mM sodium acetate trihydrate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein	分辨率 2.27 Å R-free 0.224
6YYX Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-methyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) 提交 2020-05-06	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 Q1Z (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；200 mM Bis Tris Propane, 200 mM sodium/potassium phosphate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 3-methyl-2-oxoglutarate, 18 mg/ml protein	分辨率 1.53 Å R-free 0.192
6YYY Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 4,4-dimethyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) 提交 2020-05-06	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 Q1W 2,2-dimethyl-4-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium bromide, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 4,4-dimethyl-2-oxoglutarate, 18 mg/ml protein	分辨率 2.29 Å R-free 0.244
6Z6Q Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-ethyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) 提交 2020-05-29	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	GOL GLYCEROL × 1 MN MANGANESE (II) ION × 1 QA8 (3~{R})-3-ethyl-2-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100 mM HEPES sodium, 200 mM ammonium chloride, 20% w/v PEG 6000, 1 mM manganese chloride, 2 mM 3-ethyl-2-oxoglutarate, 18 mg/ml protein	分辨率 1.81 Å R-free 0.232
6Z6R Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, N-oxalyl-alpha-methylalanine, and factor X substrate peptide fragment(39mer-4Ser) 提交 2020-05-29	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 BR BROMIDE ION × 1 GOL GLYCEROL × 1 UQK N-oxalyl-alpha-methylalanine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis Tris propane, 200 mM sodium bromide, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM N-oxalyl-alpha-methylalanine, 18 mg/ml protein	分辨率 2.13 Å R-free 0.242
7BMI Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser) 提交 2021-01-20	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 U4B 3-fluoranylpyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100 mM HEPES sodium, 200 mM ammonium chloride, 20% w/v PEG 4000, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein	分辨率 1.66 Å R-free 0.220
7BMJ Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 5-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser) 提交 2021-01-20	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 U4Q 5-fluoranylpyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium nitrate, 20% w/v PEG 3350, 1 mM manganese chloride, 18 mg/ml protein	分辨率 1.75 Å R-free 0.251
7BMJ Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 5-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser) 提交 2021-01-20	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 U4Q 5-fluoranylpyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium nitrate, 20% w/v PEG 3350, 1 mM manganese chloride, 18 mg/ml protein	分辨率 1.75 Å R-free 0.251
7E6J Aspartyl/Asparaginyl beta-hydroxylase (AspH) H725A in complex with Factor X peptide fragment (39mer-4Ser) 提交 2021-02-22	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	突变：H725A	GOL GLYCEROL × 3 PPI PROPANOIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100mM PCTP, 25% w/v PEG 1500	分辨率 1.90 Å R-free 0.213
7YB8 Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser) 提交 2022-06-29	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	GOL GLYCEROL × 2 MN MANGANESE (II) ION × 1 2HG (2R)-2-hydroxypentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M lithium chloride, 20 % w/v Polyethylene glycol 6,000, 0.1 M Tris-HCl	分辨率 1.98 Å R-free 0.248
7YB9 Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with L-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser) 提交 2022-06-29	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 329–758（430 aa）	未记录	MN MANGANESE (II) ION × 1 S2G (2S)-2-HYDROXYPENTANEDIOIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M lithium chloride, 20 % w/v Polyethylene glycol 6,000, 0.1 M Bis-Tris propane	分辨率 1.54 Å R-free 0.215
7YBA Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate 提交 2022-06-29	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 IO9 (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.1；277 K；0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350	分辨率 1.86 Å R-free 0.202
7YBB Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate and factor X-derived peptide (39mer-4Ser) 提交 2022-06-29	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 IO9 (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.02 M Sodium/potassium phosphate, 20 % w/v Polyethylene glycol 3,350, 0.1 M Bis-Tris propane	分辨率 1.68 Å R-free 0.219
7YBC Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with (S)-4-hydroxy-4-methyl-2-oxoglutarate and factor X-derived peptide (39mer-4Ser) 提交 2022-06-29	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 IOW (2~{S})-2-methyl-2-oxidanyl-4-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2 M Sodium acetate trihydrate, 20 % w/v Polyethylene glycol 3,350, 0.1 M Bis Tris propane	分辨率 1.84 Å R-free 0.199
8RE5 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735Q variant in complex with Mn, 2-oxosuberate and a Factor X derived peptide fragment 提交 2023-12-10	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 315–758（444 aa）	突变：R735Q	YQX 2-oxidanylideneoctanedioic acid × 2 MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350	分辨率 1.70 Å R-free 0.207
8RE6 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735Q variant in complex with Mn, 2-oxoglutarate and a Factor X derived peptide fragment 提交 2023-12-10	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 315–758（444 aa）	突变：R735Q	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350	分辨率 1.92 Å R-free 0.216
8RE7 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735W variant in complex with Mn, 2-oxoglutarate and a Factor X derived peptide fragment 提交 2023-12-10	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 315–758（444 aa）	突变：R735W	AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350	分辨率 1.95 Å R-free 0.242
8RE8 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived peptide fragment 提交 2023-12-10	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 315–758（444 aa）	突变：R688Q	Q1Z (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 5 MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350	分辨率 1.85 Å R-free 0.208
8RE9 Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Mn, 2-oxoglutarate and a Factor X derived peptide fragment 提交 2023-12-10	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 315–758（444 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1 PEG DI(HYDROXYETHYL)ETHER × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5 20 % v/v PEG Smear High (BCS screen)	分辨率 1.84 Å R-free 0.196
9FVU Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, thiocyanate and Factor X derived peptide fragment 提交 2024-06-28	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–758（758 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 PEG DI(HYDROXYETHYL)ETHER × 8 SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaSCN, 20% PEG 3350	分辨率 1.70 Å R-free 0.187
9FVV Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Mn, 2OG, thiocyanate and Factor X peptide fragment (39mer-4Ser) 提交 2024-06-28	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 ACT ACETATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 MN MANGANESE (II) ION × 1 SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaSCN, 20% PEG 3350	分辨率 1.60 Å R-free 0.191
9FVW Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, SIN and hydroxylated product of Factor X peptide fragment (39mer-4Ser) 提交 2024-06-28	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	SIN SUCCINIC ACID × 1 AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350	分辨率 1.90 Å R-free 0.224
9FVX Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment 提交 2024-06-28	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 331–758（428 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 7 CL CHLORIDE ION × 2 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350	分辨率 1.90 Å R-free 0.212
9FVY Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, succinate and the hudroxylated product of Factor X derived peptide fragment after O2 exposure 提交 2024-06-28	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 SIN SUCCINIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 2 FE FE (III) ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350	分辨率 1.90 Å R-free 0.199
9FVZ Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and a Factor X derived peptide fragment 提交 2024-06-28	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 331–758（428 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 6 GOL GLYCEROL × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350	分辨率 1.98 Å R-free 0.213
9FW0 Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment 提交 2024-06-28	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 331–758（428 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M Bis Tris propane pH 7.5, 0.1 M KSCN	分辨率 1.95 Å R-free 0.207
9HNZ Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and hydroxylated Factor X derived peptide fragment, 2 h O2 exposure 提交 2024-12-11	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	SIN SUCCINIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 BATCH MODE；pH 7.5；278 K；16% PEG3350, 0.1 M bis tris propane pH 7.5, 0.1 M KSCN	分辨率 2.40 Å R-free 0.237
9HO0 Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, succinate and the hydroxylated product of Factor X derived peptide fragment, 12 h O2 exposure 提交 2024-12-11	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	SIN SUCCINIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M bis-tris propane pH 7.5, 0.1 M KSCN	分辨率 2.14 Å R-free 0.232
9HO1 Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, and hydroxylated Factor X derived peptide fragment, 1.5 s O2 exposure 提交 2024-12-11	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 SIN SUCCINIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 BATCH MODE；pH 7.5；278 K；16% PEG3350, 0.1M Bis Tris propane pH 7.5, 0.1 M KSCN	分辨率 1.85 Å R-free 0.221
9HO2 Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment, excess Fe removed 提交 2024-12-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 331–758（428 aa）	未记录	AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M Bis Tris propane pH 7.5, 0.1 M KSCN	分辨率 1.83 Å R-free 0.219
9HO3 Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, nitric oxide, and Factor X peptide fragment 提交 2024-12-11	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 330–758（429 aa）	未记录	NA SODIUM ION × 1 K POTASSIUM ION × 1 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 16% PEG3350, 0.1 M KSCN	分辨率 2.39 Å R-free 0.242

共 42 个其他 PDB 条目、44 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	ASPH_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–429； UniProt 330–758

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	6yyv
沉积日期 deposition_date	2020-05-06
结构标题 title	Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 3-methyl-2-oxoglutarate
关键词 keywords	Aspartyl/asparaginyl beta-hydroxylase, Dioxygenase, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	27.51 Å
回转半径 Rg (电子) rg_electron	27.40 Å
零角强度 I(0) i0	38942600.00
分子量 molecular_weight	48228.0 kDa
排除体积 excluded_volume	60174 Å³
包络体积 envelope_volume	76730 Å³
水化壳体积 shell_volume	24272 Å³
包络直径 envelope_diameter	93.2 Å
壳层 Rg shell_rg	33.49 Å
包络 Rg envelope_rg	27.09 Å
形状 Rg shape_rg	27.38 Å
总 Rg total_rg	28.11 Å
总原子数 total_atoms	6689
残基数 n_residues	429
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	90.1 Å
Rg (实空间) rg_real	27.66 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	3.8940e+07
I(0) 误差 (实空间) i0_real_error	6.0900e+05
Rg (倒空间) rg_reciprocal	27.62 Å
I(0) (倒空间) i0_reciprocal	38940000.0000
解质量估计 total_estimate	0.8790
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.4 Å
偏度 Skewness skewness	0.394
峰度 Kurtosis kurtosis	-0.468
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4827000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.891; Smooth: 0.792

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	Aspartyl/asparaginyl beta-hydroxylase
分子量 formula_weight	49405.3 kDa
EC 编号 ec_number	1.14.11.16
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	7147

KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	(3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid
分子量 formula_weight	160.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 4 Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	408

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8. 引用文献 (1)

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晶胞边长 a length_a	48.802 Å
晶胞边长 b length_b	70.521 Å
晶胞边长 c length_c	174.488 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.770 Å
最低分辨率 resolution_low	43.620 Å
R 因子 r_factor	0.1745
R_work r_work	0.1727
R_free r_free	0.2084

fit	/app/data/saxs_computation/yy/6yyv/6yyv.fit
pddf	/app/data/pr_computation/yy/6yyv/6yyv.pr.out
profile	/app/data/saxs_computation/yy/6yyv/6yyv.dat