1h53

Binding of Phosphate and Pyrophosphate ions at the active site of human Angiogenin as revealed by X-ray Crystallography

Method: X-RAY DIFFRACTION D_max: 50.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ANGIOGENIN

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 26–147	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.2；20MM SODIUM CITRATE, 0.2M SODIUM POTASSIUM TARTARATE, 10% PEG 6000 PH 5.2	Resolution 2.00 Å R-free 0.260

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 1H53	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A4Y RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX Deposited 1998-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–147（123 aa） Chain E 25–147（123 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；THE COMPLEX WAS CRYSTALLIZED FROM 10% PEG4000, 20MM SODIUM CITRATE (PH 4.2), 0.1 AMMONIUM SULPHATE AND 25 MM DTT.	Resolution 2.00 Å R-free 0.286
1ANG CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN REVEALS THE STRUCTURAL BASIS FOR ITS FUNCTIONAL DIVERGENCE FROM RIBONUCLEASE Deposited 1994-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–147（123 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1AWZ 3D SOLUTION STRUCTURE OF HUMAN ANGIOGENIN DETERMINED BY 1H, 15N NMR SPECTROSCOPY, 30 STRUCTURES Deposited 1997-10-07	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；313 K；Ionic strength (raw mmCIF value) 150 mM；Pressure 1	Resolution not provided
1B1E CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT K40Q Deposited 1998-11-20	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 1–123（123 aa）	Mutation：K40Q	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；289 K；pH 5.2, temperature 289K	Resolution 2.00 Å R-free 0.287
1B1I CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN Deposited 1998-11-20	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 1–123（123 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 1.80 Å R-free 0.273
1B1J CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT H13A. Deposited 1998-11-20	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 1–123（123 aa）	Mutation：H13A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.319
1GV7 ARH-I, an angiogenin/RNase A chimera Deposited 2002-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–81（57 aa） Chain A 95–147（53 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；289 K；VAPOUR DIFFUSION, 16 C 10 MG/ML PROTEIN, 15 % PEG 4000, 8 % TERT-BUTANOL, 0.3 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE BUFFER, PH 5.8	Resolution 2.10 Å R-free 0.274
1H0D Crystal structure of Human Angiogenin in complex with Fab fragment of its monoclonal antibody mAb 26-2F Deposited 2002-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 25–147（123 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 8 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；30% PEG 3350 AND 0.2M LITHIUM SULPHATE PH 6.0-7.5	Resolution 2.00 Å R-free 0.272
1H52 Binding of Phosphate and Pyrophosphate ions at the active site of human Angiogenin as revealed by X-ray Crystallography Deposited 2001-05-18	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	POP PYROPHOSPHATE 2- × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；20MM SODIUM CITRATE, 0.2M SODIUM POTASSIUM TARTARATE, 10% PEG 6000 PH 5.2	Resolution 2.00 Å R-free 0.287
1HBY Binding of Phosphate and Pyrophosphate ions at the active site of human angiogenin as revealed by X-ray Crystallography Deposited 2001-04-21	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 25–147（123 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；25% PEG 6000, 0.1M MES, PH 6.0, 0.1M NACL	Resolution 2.00 Å R-free 0.230
1K58 Crystal Structure of Human Angiogenin Variant D116H Deposited 2001-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Mutation：D116H Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；sodium citrate, 2-propanol, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.70 Å R-free 0.360
1K59 Crystal Structure of Human Angiogenin Variant Q117G Deposited 2001-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Mutation：Q117G Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；289 K；sodium citrate, PEG 6000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.80 Å R-free 0.241
1K5A Crystal structure of human angiogenin double variant I119A/F120A Deposited 2001-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Mutation：I119A,F120A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；ammonium actate, sodium citrate, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.33 Å R-free 0.281
1K5B Crystal Structure of Human Angiogenin Variant des(121-123) Deposited 2001-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Mutation：DEL(121-123) Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；289 K；sodium citrate, sodium potassium tartrate, PEG 6000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.80 Å R-free 0.275
1UN3 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T44D Deposited 2003-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；15% PEG 4000, 0.02% DIOXANE, 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER, PH 5.2	Resolution 1.70 Å R-free 0.223
1UN4 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T80A Deposited 2003-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–147（123 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；15% PEG 4000, 0.02% DIOXANE, 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER, PH 5.2	Resolution 2.10 Å R-free 0.232
1UN5 ARH-II, AN ANGIOGENIN/RNASE A CHIMERA Deposited 2003-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–61（37 aa） Chain A 66–147（82 aa）	Mutation：YES Mutation：YES	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；10% PEG 6000, PH 5.4 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER	Resolution 2.60 Å R-free 0.237
2ANG CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN OF THE MET(-1) FORM Deposited 1998-11-12	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 25–147（123 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；pH 5.2	Resolution 2.00 Å R-free 0.286
4AHD Q12L - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 2.47 Å R-free 0.249
4AHD Q12L - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–147（123 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 2.47 Å R-free 0.249
4AHE K17I - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5	Resolution 2.08 Å R-free 0.300
4AHF K17E - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 2.12 Å R-free 0.285
4AHG S28N - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	TAR D(-)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5	Resolution 2.45 Å R-free 0.275
4AHH R31K - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 2.50 Å R-free 0.242
4AHI K40I - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 2.80 Å R-free 0.278
4AHJ I46V - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	TAR D(-)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 2.03 Å R-free 0.280
4AHK K54E - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5	Resolution 1.97 Å R-free 0.279
4AHK K54E - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–147（123 aa）	Mutation：YES	TAR D(-)-TARTARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5	Resolution 1.97 Å R-free 0.279
4AHL P112L - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5	Resolution 2.05 Å R-free 0.303
4AHM V113I - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	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 25–147（123 aa）	Mutation：YES	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5	Resolution 1.96 Å R-free 0.221
4AHN R121H - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis Deposited 2012-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–147（123 aa）	Mutation：YES	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 2.98 Å R-free 0.283
4AOH Structural snapshots and functional analysis of human angiogenin variants associated with Amyotrophic Lateral Sclerosis (ALS) Deposited 2012-03-27	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 24–147（124 aa） Fragment：RESIDUES 24-147	Not recorded	TAR D(-)-TARTARIC ACID × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0	Resolution 1.04 Å R-free 0.188
4B36 Crystal Structure of Human Angiogenin with an Engineered Loop Exhibits Conformational Flexibility at the Functional Regions of the Molecule Deposited 2012-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–107（83 aa） Fragment：RESIDUES 25-107,111-120,116-147 Chain A 116–147（32 aa） Fragment：RESIDUES 25-107,111-120,116-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 1.75-2.5 M NACL	Resolution 1.76 Å R-free 0.285
4B36 Crystal Structure of Human Angiogenin with an Engineered Loop Exhibits Conformational Flexibility at the Functional Regions of the Molecule Deposited 2012-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–107（83 aa） Fragment：RESIDUES 25-107,111-120,116-147 Chain B 116–147（32 aa） Fragment：RESIDUES 25-107,111-120,116-147	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 1.75-2.5 M NACL	Resolution 1.76 Å R-free 0.285
5EOP Crystal structure of human Angiogenin at 1.35 Angstroms resolution Deposited 2015-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–146（121 aa） Fragment：UNP residues 26-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；289 K；Malic acid/NaOH pH 7.0 PEG 3350	Resolution 1.35 Å R-free 0.192
5EPZ Human Angiogenin in complex with sulphate anions at a basic solution Deposited 2015-11-12	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 26–145（120 aa） Fragment：UNP residues 26-145	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；289 K；0.1 M Tris/HCl buffer pH 8.0, 2.4 M ammonium sulphate	Resolution 1.85 Å R-free 0.217
5EQO Human Angiogenin in complex with sulphate anions at an acidic solution Deposited 2015-11-13	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 25–145（121 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；289 K；0.1 M sodium cacodylate pH 6.0 2.0 M ammonium sulphate	Resolution 2.40 Å R-free 0.250
5M9A Human angiogenin PD variant H13R Deposited 2016-11-01	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 25–147（123 aa）	Mutation：H13R	TAR D(-)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Na/K tartrate 20% PEG 3350	Resolution 1.95 Å R-free 0.297
5M9C Human angiogenin ALS variant K40R Deposited 2016-11-01	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 25–147（123 aa）	Mutation：K40R	TAR D(-)-TARTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.4 M Na/K tartrate 0.1 M Na citrate 20 % PEG 4000	Resolution 2.05 Å R-free 0.231
5M9G Human angiogenin PD variant K54R Deposited 2016-11-01	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 25–147（123 aa）	Mutation：K54R	TAR D(-)-TARTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.2 M Na/K tartrate 0.1 M HEPES 3% propanol 20% PEG 8000	Resolution 2.28 Å R-free 0.271
5M9J Human angiogenin PD variant K60E Deposited 2016-11-01	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 25–147（123 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.2 M Na/K tartrate 0.1 M Na cacodylate 25% PEG 4000	Resolution 1.90 Å R-free 0.216
5M9M Human angiogenin PD variant Q77P Deposited 2016-11-01	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 25–147（123 aa）	Not recorded	SO4 SULFATE ION × 2 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350	Resolution 1.65 Å R-free 0.270
5M9M Human angiogenin PD variant Q77P Deposited 2016-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–147（123 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350	Resolution 1.65 Å R-free 0.270
5M9M Human angiogenin PD variant Q77P Deposited 2016-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 25–147（123 aa）	Not recorded	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350	Resolution 1.65 Å R-free 0.270
5M9M Human angiogenin PD variant Q77P Deposited 2016-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 25–147（123 aa）	Not recorded	SO4 SULFATE ION × 4 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350	Resolution 1.65 Å R-free 0.270
5M9P Human angiogenin ALS variant T80S Deposited 2016-11-02	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 25–147（123 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.2 M ammonium sulphate 0.1 M bis-tris propane 25% PEG 3350	Resolution 1.80 Å R-free 0.285
5M9Q Human angiogenin PD variant R95Q Deposited 2016-11-02	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 25–147（123 aa）	Not recorded	SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 3 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2 M ammonium sulphate 0.1 M Na cacodylate 30% PEG 8000	Resolution 1.35 Å R-free 0.179
5M9R Human angiogenin ALS variant F100I Deposited 2016-11-02	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 25–147（123 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 1 TLA L(+)-TARTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.2 M Na/K tartrate 0.1 M Na cacodylate 20% PEG 4000	Resolution 1.44 Å R-free 0.195
5M9R Human angiogenin ALS variant F100I Deposited 2016-11-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–147（123 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.2 M Na/K tartrate 0.1 M Na cacodylate 20% PEG 4000	Resolution 1.44 Å R-free 0.195
5M9S Human angiogenin ALS variant V103I Deposited 2016-11-02	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 25–147（123 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.2 M Na/K tartrate 0.1 M MES 20% PEG 4000	Resolution 1.85 Å R-free 0.264
5M9T Human angiogenin ALS variant H114R Deposited 2016-11-02	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 25–147（123 aa）	Not recorded	GOL GLYCEROL × 1 BO4 BORATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.01 M Na borate 1.1 M Na citrate	Resolution 2.20 Å R-free 0.236
5M9T Human angiogenin ALS variant H114R Deposited 2016-11-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–147（123 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.01 M Na borate 1.1 M Na citrate	Resolution 2.20 Å R-free 0.236
5M9V Human angiogenin PD/ALS variant R121C Deposited 2016-11-02	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 25–147（123 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.2 M Na/K tartrate 0.1 M bis-tris propane 16% PEG 4000	Resolution 1.70 Å R-free 0.239
7NPM X-ray structure of the adduct formed upon reaction of oxaliplatin with human angiogenin Deposited 2021-02-27	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 AAA 26–146（121 aa） Fragment：UNP residues 26-166	Not recorded	PT PLATINUM (II) ION × 3 TAR D(-)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；298 K；10 % PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate	Resolution 1.86 Å R-free 0.254
7PNJ Human Angiogenin quardruple mutant-S28AT36AS37AS87A Deposited 2021-09-07	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 25–145（121 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；100 mM SODIUM CITRATE PH 5.6, 25% (w/v) PEG 4000	Resolution 3.10 Å R-free 0.276
7PNP Human Angiogenin mutant-S28A Deposited 2021-09-07	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 25–147（123 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Malic acid/NaOH pH 7.0, PEG 3350	Resolution 1.80 Å R-free 0.254
7PNR Human Angiogenin mutant-S28AT36AS37A Deposited 2021-09-07	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 25–145（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Malic acid/NaOH pH 7.0, PEG 3350	Resolution 1.60 Å R-free 0.201
8AF0 Crystal structure of human angiogenin and RNA duplex Deposited 2022-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 25–147（123 aa） Chain B 25–147（123 aa）	Mutation：H114A Mutation：H114A	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；200 mM NaCl, 20 % (w/v) PEG6000, 100 mM Hepes pH 7.0	Resolution 2.43 Å R-free 0.268
9BDL 80S ribosome with angiogenin Deposited 2024-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain ANG 1–147（147 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9BDN 80S ribosome with angiogenin and tRNAAla Deposited 2024-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 85-meric	Chain ANG 1–147（147 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9BDP 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla Deposited 2024-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 86-meric	Chain ANG 1–147（147 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

53 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANGI_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–123； UniProt 26–147

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	1h53
Deposition date deposition_date	2001-05-18
Structure title title	Binding of Phosphate and Pyrophosphate ions at the active site of human Angiogenin as revealed by X-ray Crystallography
Keywords keywords	ANGIOGENIN, RIBONUCLEASE, PHOSPHATE, PYROPHOSPHATE, HYDROLASE; HYDROLASE
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	15.42 Å
Radius of gyration Rg (electron density) rg_electron	14.29 Å
Forward intensity I(0) i0	4604700.00
Molecular weight molecular_weight	14127.0 kDa
Excluded volume excluded_volume	17192 Å³
Envelope volume envelope_volume	19794 Å³
Hydration-shell volume shell_volume	11948 Å³
Envelope diameter envelope_diameter	48.4 Å
Shell Rg shell_rg	19.90 Å
Envelope Rg envelope_rg	14.64 Å
Shape Rg shape_rg	14.28 Å
Total Rg total_rg	15.38 Å
Total atoms total_atoms	989
Residues n_residues	121
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	50.8 Å
Rg (real space) rg_real	15.37 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	4.6050e+06
I(0) uncertainty (real space) i0_real_error	5.6030e+04
Rg (reciprocal space) rg_reciprocal	15.38 Å
I(0) (reciprocal space) i0_reciprocal	4605000.0000
Solution quality estimate total_estimate	0.8848
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.360
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1030000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.984

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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	ANGIOGENIN
Molecular weight formula_weight	14080.9 kDa
EC 编号 ec_number	3.1.27.-
Mutation mutation	YES
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	1036

QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDGSIFRRP

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

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 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	47

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1h53a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.5 — RNase A-like
Superfamily Superfamily superfamily	d.5.1 — RNase A-like
Family Family family	d.5.1.1 — Ribonuclease A-like

CATH v4.4 (1 domains)

Domain ID domain_id	1h53A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	130 — P-30 Protein
Homologous superfamily homologous superfamily	10 — Ribonuclease A-like domain

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8. Citations (2)

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Unit-cell length a length_a	85.383 Å
Unit-cell length b length_b	37.538 Å
Unit-cell length c length_c	38.534 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2600

fit	/app/data/saxs_computation/h5/1h53/1h53.fit
pddf	/app/data/pr_computation/h5/1h53/1h53.pr.out
profile	/app/data/saxs_computation/h5/1h53/1h53.dat