3ne4

1.8 Angstrom structure of intact native wild-type alpha-1-antitrypsin

Method: X-RAY DIFFRACTION D_max: 82.2 Å Quality: GOOD

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

Alpha-1-antitrypsin

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 48–418	Fragment：UNP residues 48-418	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MMT Buffer, 20 % PEG 1500 and N-[4-hydroxy-3-methyl-5- [(1H-1,2,4,5-tetrazol-3-yl)sulfanyl] phenyl]-4-methylbenzenesulfonamide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.233

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 3NE4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ATU UNCLEAVED ALPHA-1-ANTITRYPSIN Deposited 1997-05-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 45–418（374 aa）	Mutation：F51L, T59A, T68A, A70G, M374I, S381A, K387R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.70 Å
1D5S CRYSTAL STRUCTURE OF CLEAVED ANTITRYPSIN POLYMER Deposited 1999-10-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 44–377（334 aa） Fragment：N-TERMINAL FRAGMENT Chain B 378–418（41 aa） Fragment：C-TERMINAL FRAGMENT	Mutation：M358R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；PEG 4000 sodium citrate buffer t-butanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.262
1EZX CRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX Deposited 2000-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 48–382（335 aa） Fragment：N-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359 Chain B 383–418（36 aa） Fragment：C-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 3350, sodium citrate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.239
1HP7 A 2.1 ANGSTROM STRUCTURE OF AN UNCLEAVED ALPHA-1-ANTITRYPSIN SHOWS VARIABILITY OF THE REACTIVE CENTER AND OTHER LOOPS Deposited 2000-12-12	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 25–418（394 aa）	Mutation：A70G	ZN ZINC ION × 5 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.273
1HP7 A 2.1 ANGSTROM STRUCTURE OF AN UNCLEAVED ALPHA-1-ANTITRYPSIN SHOWS VARIABILITY OF THE REACTIVE CENTER AND OTHER LOOPS Deposited 2000-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–418（394 aa）	Mutation：A70G	ZN ZINC ION × 10 BME BETA-MERCAPTOETHANOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.273
1HP7 A 2.1 ANGSTROM STRUCTURE OF AN UNCLEAVED ALPHA-1-ANTITRYPSIN SHOWS VARIABILITY OF THE REACTIVE CENTER AND OTHER LOOPS Deposited 2000-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–418（394 aa）	Mutation：A70G	ZN ZINC ION × 10 BME BETA-MERCAPTOETHANOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.273
1IZ2 Interactions causing the kinetic trap in serpin protein folding Deposited 2002-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–418（394 aa）	Mutation：F51L/T59A/T68A/A70G/R101H/V364A/M374I/E376D/S381A/K387R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Ammonium Sulfate 1.8M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.278
1KCT ALPHA1-ANTITRYPSIN Deposited 1996-08-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–418（394 aa）	Mutation：T59A, T68A, A70G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 3.46 Å
1OO8 CRYSTAL STRUCTURE OF A1PI-PITTSBURGH IN THE NATIVE CONFORMATION Deposited 2003-03-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa） Fragment：RESIDUES 26-418	Mutation：F51L, T59A, T68A, A70G, C232S, M358R, M374I, S381A, K387R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；292 K；0.2M TRI-POTASSIUM CITRATE, 20% PEG-3350, pH 6.30, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K	Resolution 2.65 Å R-free 0.193
1OPH NON-COVALENT COMPLEX BETWEEN ALPHA-1-PI-PITTSBURGH AND S195A TRYPSIN Deposited 2003-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–418（393 aa） Fragment：alpha-1-antitrypsin (RESIDUES 26-418)	Mutation：F51L, T59A, T68A, A70G, C232S, M358R, M274I, S381A, K387R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；291 K；0.2 M tri-K-citrate, 17.5% PEG 3350, 2% GLYCEROL, pH 8.30, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.229
1OPH NON-COVALENT COMPLEX BETWEEN ALPHA-1-PI-PITTSBURGH AND S195A TRYPSIN Deposited 2003-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–418（393 aa） Fragment：alpha-1-antitrypsin (RESIDUES 26-418)	Mutation：F51L, T59A, T68A, A70G, C232S, M358R, M274I, S381A, K387R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；291 K；0.2 M tri-K-citrate, 17.5% PEG 3350, 2% GLYCEROL, pH 8.30, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.229
1PSI Intact recombined alpha1-antitrypsin mutant PHE 51 to LEU Deposited 1996-06-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：F51L Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；24% PEG, 0.2 M SODIUM ACETATE, 0.1 M TRIS.HCL, PH 6.0, 0.002 M FESO4, 25 DEG CELSIUS	Resolution 2.92 Å R-free 0.288
1QLP 2.0 ANGSTROM STRUCTURE OF INTACT ALPHA-1-ANTITRYPSIN: A CANONICAL TEMPLATE FOR ACTIVE SERPINS Deposited 1999-09-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；24% PEG 4000, 0.2 M SODIUM ACETATE, 0.1M TRIS-HCL PH 6.0, 2MM FESO4.7H20	Resolution 2.00 Å R-free 0.266
1QMB Cleaved alpha-1-antitrypsin polymer Deposited 1999-09-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 49–69（21 aa） Fragment：RESIDUES 49-69,71-302,304-376 Chain A 71–302（232 aa） Fragment：RESIDUES 49-69,71-302,304-376 Chain A 304–376（73 aa） Fragment：RESIDUES 49-69,71-302,304-376 Chain B 377–418（42 aa） Fragment：RESIDUES 377-418	Mutation：YES Mutation：YES Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2M TRI-SODIUM CITRATE, 0.1M TRIS, PH 8.5, 30% PEG 400	Resolution 2.60 Å R-free 0.258
2D26 Active site distortion is sufficient for proteinase inhibit second crystal structure of covalent serpin-proteinase complex Deposited 2005-09-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–382（358 aa） Fragment：residues 1-358 Chain B 383–418（36 aa） Fragment：residues 359-394	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；291 K；PEG3350, pH 8.10, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.30 Å R-free 0.312
2QUG Crystal structure of alpha-1-antitrypsin, crystal form A Deposited 2007-08-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–418（394 aa）	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；295 K；29% PEG 3350, 400 mM NaF, vapor diffusion, hanging drop, temperature 295K	Resolution 2.00 Å R-free 0.275
3CWL Crystal structure of alpha-1-antitrypsin, crystal form B Deposited 2008-04-22	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 25–418（394 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；295 K；27% PEG 4000, 0.2M Sodium Acetate, 100mM Tris-HCl, pH 8.4, vapor diffusion, hanging drop, temperature 295K, pH 8.40	Resolution 2.44 Å R-free 0.264
3CWM Crystal structure of alpha-1-antitrypsin complexed with citrate Deposited 2008-04-22	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 25–418（394 aa）	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 8.4；295 K；27% PEG 4000, 0.2M Sodium Acetate, 100mM Tris-HCl, pH 8.4, vapor diffusion, hanging drop, temperature 295K	Resolution 2.51 Å R-free 0.271
3DRM 2.2 Angstrom Crystal Structure of Thr114Phe Alpha1-Antitrypsin Deposited 2008-07-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：T114F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, Li2SO4, Tris/HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K	Resolution 2.20 Å R-free 0.272
3DRU Crystal Structure of Gly117Phe Alpha1-Antitrypsin Deposited 2008-07-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：G117F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, Li2SO4, Tris/HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.20 Å R-free 0.290
3DRU Crystal Structure of Gly117Phe Alpha1-Antitrypsin Deposited 2008-07-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–418（393 aa）	Mutation：G117F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, Li2SO4, Tris/HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.20 Å R-free 0.290
3DRU Crystal Structure of Gly117Phe Alpha1-Antitrypsin Deposited 2008-07-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–418（393 aa）	Mutation：G117F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, Li2SO4, Tris/HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.20 Å R-free 0.290
3NDD Cleaved antitrypsin with P10 Pro, and P9-P6 Asp Deposited 2010-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 46–382（337 aa） Fragment：P1 cleaved antitrypsin, nterm, UNP residues 46-382 Chain B 383–418（36 aa） Fragment：P1 cleaved antitrypsin, cterm, UNP residues 383-418	Mutation：C232A, G349P, A350D, M351D, F352D, L353D, M358R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；295 K；0.1M MES/NaOH, 30% PEG 400, 35% glycerol, pH 6, VAPOR DIFFUSION, temperature 295K	Resolution 1.50 Å R-free 0.211
3NDF Cleaved antitrypsin with P8-P6 Asp Deposited 2010-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 46–382（337 aa） Fragment：P1 cleaved antitrypsin, nterm, UNP residues 46-382 Chain B 383–418（36 aa） Fragment：P1 cleaved antitrypsin, cterm, UNP residues 383-418	Mutation：C232A, M351D, F352D, L353D, M358R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；295 K；0.12M Alcohols (Morpheus), 0.1M Buffer 1, 13.3% PEG 550MME, 6.6% PEG 20000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.70 Å R-free 0.268
3T1P Crystal structure of an alpha-1-antitrypsin trimer Deposited 2011-07-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 48–418（371 aa） Fragment：unp residues 48-418	Mutation：C256S, S316C, T363C, M382R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% (w/w) ethanol, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.90 Å R-free 0.297
4PYW 1.92 angstrom crystal structure of A1AT:TTAI ternary complex Deposited 2014-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–418（393 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；26% PEG3350, 0.1 M Bis-Tris pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.91 Å R-free 0.225
5IO1 CRYSTAL STRUCTURE OF RECOMBINANT HUMAN Z ALPHA-1-ANTITRYPSIN Deposited 2016-03-08	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 29–418（390 aa） Fragment：UNP residues 29-418	Mutation：E342L, T345C, M358A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；20-30% PEG8000, 0.2M NACL, 0.1M MES, PH 6.5, EVAPORATION, TEMPERATURE 298K	Resolution 3.34 Å R-free 0.275
5IO1 CRYSTAL STRUCTURE OF RECOMBINANT HUMAN Z ALPHA-1-ANTITRYPSIN Deposited 2016-03-08	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 29–418（390 aa） Fragment：UNP residues 29-418	Mutation：E342L, T345C, M358A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；20-30% PEG8000, 0.2M NACL, 0.1M MES, PH 6.5, EVAPORATION, TEMPERATURE 298K	Resolution 3.34 Å R-free 0.275
5NBU Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations Deposited 2017-03-02	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 43–418（376 aa）	Mutation：F51L, T59A, T68A, A70G, C232S, M374I, S381A, K387R	GOL GLYCEROL × 2 OXM OXAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000, carboxylic acid mixture	Resolution 1.67 Å R-free 0.228
5NBV Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations Deposited 2017-03-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–418（376 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000, carboxylic acid mixture	Resolution 1.73 Å R-free 0.259
6HX4 Fab fragment of a native monomer-selective antibody in complex with alpha-1-antitrypsin Deposited 2018-10-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 24–418（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；15% PEG 4000, 0.1M sodium cacodylate pH 6	Resolution 2.95 Å R-free 0.277
6HX4 Fab fragment of a native monomer-selective antibody in complex with alpha-1-antitrypsin Deposited 2018-10-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–418（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；15% PEG 4000, 0.1M sodium cacodylate pH 6	Resolution 2.95 Å R-free 0.277
6I3Z Fab fragment of an antibody selective for wild-type alpha-1-antitrypsin in complex with its antigen Deposited 2018-11-08	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 A 26–377（352 aa） Chain B 378–418（41 aa）	Not recorded	NA SODIUM ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20% PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES pH 7.5	Resolution 3.10 Å R-free 0.307
6I4V Alpha-1-antitrypsin Queen's (K154N) variant Deposited 2018-11-12	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 26–418（393 aa）	Mutation：K154N	GLY GLYCINE × 2 H3B 3-trimethylsilylpropane-1-sulfonic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；20% PEG 1500, 0.1M SPG (succinate-phosphate-glycine), 0.5mM DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid)	Resolution 1.78 Å R-free 0.213
6I7U Alpha-1-antitrypsin (Ala250Met) in the native conformation Deposited 2018-11-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：A250M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；22.5% PEG 1500, 0.1M SPG (succinate-phosphate-glycine) pH 5.5	Resolution 1.55 Å R-free 0.211
6IAY Alpha-1-antitrypsin Queen's (Lys154Asn) variant Deposited 2018-11-28	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 26–418（393 aa）	Mutation：K154N	GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；22.5% PEG 1500, 0.1M SPG (succinate-phosphate-glycine) pH 5.75	Resolution 1.90 Å R-free 0.241
6ROD Alpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native conformation Deposited 2019-05-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：S36R, E78R, E266R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；293 K；22.5% PEG 1500, 0.1M SPG (succinate-phosphate-glycine) pH 5.25	Resolution 1.85 Å R-free 0.223
7AEL alpha 1-antitrypsin (C232S) complexed with GSK716 Deposited 2020-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 26–418（393 aa）	Not recorded	R7Z ~{N}-[(1~{S},2~{R})-1-(3-fluoranyl-2-methyl-phenyl)-1-oxidanyl-pentan-2-yl]-2-oxidanylidene-1,3-dihydroindole-4-carboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；22% PEG1500, 0.2M MES pH 6.0	Resolution 1.76 Å R-free 0.224
7API THE S VARIANT OF HUMAN ALPHA1-ANTITRYPSIN, STRUCTURE AND IMPLICATIONS FOR FUNCTION AND METABOLISM Deposited 1988-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–382（347 aa） Chain B 383–418（36 aa）	Not recorded	CYS CYSTEINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
7NPK ALPHA-1 ANTITRYPSIN C232S COMPLEXED WITH CMPD3 Deposited 2021-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–417（392 aa）	Not recorded	GOL GLYCEROL × 2 UL2 N-((1S,2R)-1-hydroxy-1-(o-tolyl)pentan-2-yl)-2-oxo-2,3-dihydrobenzo[d]oxazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；14% w/v PEG1500, 0.2M MES pH6.0	Resolution 1.83 Å R-free 0.233
7NPL ALPHA-1 ANTITRYPSIN (C232S) COMPLEXED WITH cmpd 11 Deposited 2021-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Not recorded	UKZ N-((1S,2R)-1-(3-chloro-2-methylphenyl)-1-hydroxypentan-2-yl)-2-oxoindoline-4-carboxamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；14% PEG1500 0.1M MES pH6.0	Resolution 1.82 Å R-free 0.218
8API THE S VARIANT OF HUMAN ALPHA1-ANTITRYPSIN, STRUCTURE AND IMPLICATIONS FOR FUNCTION AND METABOLISM Deposited 1988-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–382（347 aa） Chain B 383–418（36 aa）	Not recorded	CYS CYSTEINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
8P4J Alpha-1-antitrypsin - Sydney variant (G192C) Deposited 2023-05-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：G192C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1M MIB pH 5.5 25% PEG 1500	Resolution 1.91 Å R-free 0.253
8P4U Alpha-1-antitrypsin - Sydney variant (G192C) Deposited 2023-05-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1M MIB pH 5.5 25% PEG 1500	Resolution 2.40 Å R-free 0.254
8PI2 Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser) Deposited 2023-06-20	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 26–418（393 aa）	Mutation：C232S	GLY GLYCINE × 1 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；294 K；0.1M malonate-imidazole-borate pH5.75, 25% PEG1500	Resolution 1.48 Å R-free 0.195
8QZ5 Alpha-1-antitrypsin (Tyr244Phe) in the native conformation Deposited 2023-10-26	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 26–418（393 aa）	Mutation：Y244F Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；25% PEG 1500, 0.1M SPG (succinate-phosphate-glycine) pH 5.75	Resolution 1.69 Å R-free 0.213
8R13 Alpha-1-antitrypsin (Met374Phe) in the native conformation Deposited 2023-11-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：M374F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；22.5% PEG 1500, 0.1M MIB (malonate-imidazole-borate) pH 5.25	Resolution 1.95 Å R-free 0.235
8R21 Alpha-1-antitrypsin (Ile340Trp) in the native conformation Deposited 2023-11-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–418（393 aa）	Mutation：I340W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；293 K；0.1M SPG (succinate-phosphate-glycine) pH 5.25, 17.5% PEG1500	Resolution 2.88 Å R-free 0.242
8R21 Alpha-1-antitrypsin (Ile340Trp) in the native conformation Deposited 2023-11-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–418（393 aa）	Mutation：I340W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；293 K；0.1M SPG (succinate-phosphate-glycine) pH 5.25, 17.5% PEG1500	Resolution 2.88 Å R-free 0.242
9API THE S VARIANT OF HUMAN ALPHA1-ANTITRYPSIN, STRUCTURE AND IMPLICATIONS FOR FUNCTION AND METABOLISM Deposited 1988-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–382（347 aa） Chain B 383–418（36 aa）	Not recorded	CYS CYSTEINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
9GGP Alpha-1-antitrypsin in complex with the Fab fragment of an anti-polymer antibody Deposited 2024-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–418（393 aa） Chain B 26–418（393 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；293 K；0.2 M Ammonium citrate dibasic 20% w/v Polyethylene glycol 3,350 pH 5.1	Resolution 1.84 Å R-free 0.206
9HUD Alpha-1-antitrypsin in the cleaved conformation in complex with a conformationally nonselective Fab fragment Deposited 2024-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–378（353 aa） Chain B 379–418（40 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GLY GLYCINE × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M sodium HEPES, MOPS 0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine 40% v/v Glycerol; 20% w/v PEG 4000	Resolution 2.42 Å R-free 0.247
9HUD Alpha-1-antitrypsin in the cleaved conformation in complex with a conformationally nonselective Fab fragment Deposited 2024-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 26–378（353 aa） Chain D 379–418（40 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 GLY GLYCINE × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 LYS LYSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M sodium HEPES, MOPS 0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine 40% v/v Glycerol; 20% w/v PEG 4000	Resolution 2.42 Å R-free 0.247
9VDI Crystal structure of the recombinant A1-antitrypsin F51L/M351V/M358V triple mutant Deposited 2025-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 47–418（372 aa）	Mutation：F51L,M351V,M358V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate, 0.1 M Tris (pH 8.5), and 25% (w/v) PEG 3350	Resolution 2.60 Å R-free 0.254
9VDI Crystal structure of the recombinant A1-antitrypsin F51L/M351V/M358V triple mutant Deposited 2025-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 47–418（372 aa）	Mutation：F51L,M351V,M358V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate, 0.1 M Tris (pH 8.5), and 25% (w/v) PEG 3350	Resolution 2.60 Å R-free 0.254

45 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A1AT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 54–424； UniProt 48–418

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	3ne4
Deposition date deposition_date	2010-06-08
Structure title title	1.8 Angstrom structure of intact native wild-type alpha-1-antitrypsin
Keywords keywords	alpha1-antitrypsin, serpin, lung disease, liver disease, polymerisation, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
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	22.85 Å
Radius of gyration Rg (electron density) rg_electron	21.56 Å
Forward intensity I(0) i0	27273000.00
Molecular weight molecular_weight	41609.0 kDa
Excluded volume excluded_volume	52791 Å³
Envelope volume envelope_volume	61905 Å³
Hydration-shell volume shell_volume	23987 Å³
Envelope diameter envelope_diameter	83.5 Å
Shell Rg shell_rg	28.53 Å
Envelope Rg envelope_rg	21.91 Å
Shape Rg shape_rg	21.51 Å
Total Rg total_rg	22.62 Å
Total atoms total_atoms	2935
Residues n_residues	370
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	82.2 Å
Rg (real space) rg_real	22.81 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.7270e+07
I(0) uncertainty (real space) i0_real_error	4.0440e+05
Rg (reciprocal space) rg_reciprocal	22.82 Å
I(0) (reciprocal space) i0_reciprocal	27270000.0000
Solution quality estimate total_estimate	0.8446
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.346
Kurtosis Kurtosis kurtosis	-0.238
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7405000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ne4a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

CATH v4.4 (2 domains)

Domain ID domain_id	3ne4A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

Domain ID domain_id	3ne4A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

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8. Citations (1)

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Unit-cell length a length_a	114.380 Å
Unit-cell length b length_b	38.940 Å
Unit-cell length c length_c	88.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	42.110 Å
R factor r_factor	0.1896
R_work r_work	0.1872
R_free r_free	0.2328

Description description	Alpha-1-antitrypsin
Molecular weight formula_weight	47619.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3167

1.8 Angstrom structure of intact native wild-type alpha-1-antitrypsin

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

Alpha-1-antitrypsin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	217

fit	/app/data/saxs_computation/ne/3ne4/3ne4.fit
pddf	/app/data/pr_computation/ne/3ne4/3ne4.pr.out
profile	/app/data/saxs_computation/ne/3ne4/3ne4.dat