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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. Protein Identity and Related Structures Protein Identity & Related Structures

Aspartyl/asparaginyl beta-hydroxylase

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 330–758	Not recorded	MN MANGANESE (II) ION × 1 Q1Z (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：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	Resolution 1.77 Å R-free 0.208

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 6YYV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5APA Crystal structure of human aspartate beta-hydroxylase isoform a Deposited 2015-09-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 562–758（197 aa） Fragment：UNP RESIDUES 562-758	Not recorded	NI NICKEL (II) ION × 1 LMR (2S)-2-hydroxybutanedioic acid × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 50MM SODIUM MALATE, 20% PEG3350, 3% DEXTRAN SULFATE, 20MM NISO4	Resolution 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) Deposited 2016-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 330–758（429 aa） Fragment：UNP residues 330-758	Not recorded	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；100mM SPG buffer, 25% PEG 1500, 2mM NOG, 1mM MnCl2, 18mg/ml protein	Resolution 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) Deposited 2016-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 330–758（429 aa） Fragment：UNP Residues 330-758	Not recorded	MN MANGANESE (II) ION × 1 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 1 BR BROMIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.24 Å R-free 0.208
5JZ6 Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese and L-malate Deposited 2016-05-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 GOL GLYCEROL × 4 LMR (2S)-2-hydroxybutanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2016-05-16	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.10 Å R-free 0.216
5JZA Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese and N-oxalylglycine Deposited 2016-05-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 GOL GLYCEROL × 4 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2016-05-17	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2018-12-18	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 330–758（429 aa）	Mutation：H679A	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.63 Å R-free 0.200
6Q9I Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Factor X peptide fragment (39mer-4Ser) Deposited 2018-12-18	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 330–758（429 aa）	Mutation：H679A	FMT FORMIC ACID × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium formate, 20 % w/v PEG 3350	Resolution 1.85 Å R-free 0.223
6QA5 Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in the apo form Deposited 2018-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 301–729（429 aa）	Mutation：H679A	ACT ACETATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2019-04-30	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2019-04-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.29 Å R-free 0.235
6YYU Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 2-oxoglutarate Deposited 2020-05-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 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	Resolution 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) Deposited 2020-05-06	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 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	Resolution 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) Deposited 2020-05-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 Q1Z (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2020-05-06	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 Q1W 2,2-dimethyl-4-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2020-05-29	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 330–758（429 aa）	Not recorded	GOL GLYCEROL × 1 MN MANGANESE (II) ION × 1 QA8 (3~{R})-3-ethyl-2-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2020-05-29	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 BR BROMIDE ION × 1 GOL GLYCEROL × 1 UQK N-oxalyl-alpha-methylalanine × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2021-01-20	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 U4B 3-fluoranylpyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2021-01-20	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 U4Q 5-fluoranylpyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium nitrate, 20% w/v PEG 3350, 1 mM manganese chloride, 18 mg/ml protein	Resolution 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) Deposited 2021-01-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 U4Q 5-fluoranylpyridine-2,4-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium nitrate, 20% w/v PEG 3350, 1 mM manganese chloride, 18 mg/ml protein	Resolution 1.75 Å R-free 0.251
7E6J Aspartyl/Asparaginyl beta-hydroxylase (AspH) H725A in complex with Factor X peptide fragment (39mer-4Ser) Deposited 2021-02-22	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 330–758（429 aa）	Mutation：H725A	GOL GLYCEROL × 3 PPI PROPANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100mM PCTP, 25% w/v PEG 1500	Resolution 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) Deposited 2022-06-29	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 330–758（429 aa）	Not recorded	GOL GLYCEROL × 2 MN MANGANESE (II) ION × 1 2HG (2R)-2-hydroxypentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2022-06-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 329–758（430 aa）	Not recorded	MN MANGANESE (II) ION × 1 S2G (2S)-2-HYDROXYPENTANEDIOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2022-06-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 IO9 (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；277 K；0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350	Resolution 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) Deposited 2022-06-29	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 330–758（429 aa）	Not recorded	MN MANGANESE (II) ION × 1 IO9 (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2022-06-29	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 330–758（429 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2023-12-10	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 315–758（444 aa）	Mutation：R735Q	YQX 2-oxidanylideneoctanedioic acid × 2 MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2023-12-10	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 315–758（444 aa）	Mutation：R735Q	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350	Resolution 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 Deposited 2023-12-10	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 315–758（444 aa）	Mutation：R735W	AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350	Resolution 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 Deposited 2023-12-10	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 315–758（444 aa）	Mutation：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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350	Resolution 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 Deposited 2023-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 315–758（444 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1 PEG DI(HYDROXYETHYL)ETHER × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5 20 % v/v PEG Smear High (BCS screen)	Resolution 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 Deposited 2024-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–758（758 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 PEG DI(HYDROXYETHYL)ETHER × 8 SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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) Deposited 2024-06-28	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 330–758（429 aa）	Not recorded	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 crystallization conditions 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	Resolution 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) Deposited 2024-06-28	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 330–758（429 aa）	Not recorded	SIN SUCCINIC ACID × 1 AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2024-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 331–758（428 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 7 CL CHLORIDE ION × 2 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2024-06-28	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 330–758（429 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2024-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 331–758（428 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 6 GOL GLYCEROL × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2024-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 331–758（428 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M Bis Tris propane pH 7.5, 0.1 M KSCN	Resolution 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 Deposited 2024-12-11	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 330–758（429 aa）	Not recorded	SIN SUCCINIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；278 K；16% PEG3350, 0.1 M bis tris propane pH 7.5, 0.1 M KSCN	Resolution 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 Deposited 2024-12-11	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 330–758（429 aa）	Not recorded	SIN SUCCINIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M bis-tris propane pH 7.5, 0.1 M KSCN	Resolution 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 Deposited 2024-12-11	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 330–758（429 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 SIN SUCCINIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；278 K；16% PEG3350, 0.1M Bis Tris propane pH 7.5, 0.1 M KSCN	Resolution 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 Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 331–758（428 aa）	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M Bis Tris propane pH 7.5, 0.1 M KSCN	Resolution 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 Deposited 2024-12-11	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 330–758（429 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 16% PEG3350, 0.1 M KSCN	Resolution 2.39 Å R-free 0.242

42 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ASPH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–429； UniProt 330–758

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6yyv
Deposition date deposition_date	2020-05-06
Structure title title	Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 3-methyl-2-oxoglutarate
Keywords keywords	Aspartyl/asparaginyl beta-hydroxylase, Dioxygenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.51 Å
Radius of gyration Rg (electron density) rg_electron	27.40 Å
Forward intensity I(0) i0	38942600.00
Molecular weight molecular_weight	48228.0 kDa
Excluded volume excluded_volume	60174 Å³
Envelope volume envelope_volume	76730 Å³
Hydration-shell volume shell_volume	24272 Å³
Envelope diameter envelope_diameter	93.2 Å
Shell Rg shell_rg	33.49 Å
Envelope Rg envelope_rg	27.09 Å
Shape Rg shape_rg	27.38 Å
Total Rg total_rg	28.11 Å
Total atoms total_atoms	6689
Residues n_residues	429
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.1 Å
Rg (real space) rg_real	27.66 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	3.8940e+07
I(0) uncertainty (real space) i0_real_error	6.0900e+05
Rg (reciprocal space) rg_reciprocal	27.62 Å
I(0) (reciprocal space) i0_reciprocal	38940000.0000
Solution quality estimate total_estimate	0.8790
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.468
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4827000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria 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. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Aspartyl/asparaginyl beta-hydroxylase
Molecular weight formula_weight	49405.3 kDa
EC 编号 ec_number	1.14.11.16
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7147

KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI

来源 Source

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

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	(3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid
Molecular weight formula_weight	160.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	408

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8. Citations (1)

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Unit-cell length a length_a	48.802 Å
Unit-cell length b length_b	70.521 Å
Unit-cell length c length_c	174.488 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	43.620 Å
R factor 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