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5nbv

Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations

Method: X-RAY DIFFRACTION Dmax: 77.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-1-antitrypsin

Homo sapiens

UniProt P01009

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 43–418 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

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 5NBV 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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：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 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） 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 ligand/ion 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 ligand/ion 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 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：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 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 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 ligand/ion 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 ligand/ion 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 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) 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 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：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 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：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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
3NE4 1.8 Angstrom structure of intact native wild-type alpha-1-antitrypsin Deposited 2010-06-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–418（371 aa） Fragment：UNP residues 48-418
Not recorded No recorded non-water small molecule 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
3T1P Crystal structure of an alpha-1-antitrypsin trimer Deposited 2011-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion 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
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 ligand/ion 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 ligand/ion 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 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：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 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：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 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：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 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 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 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：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 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：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 ligand/ion 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 ligand/ion 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 ligand/ion 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 2–377； UniProt 43–418

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

SAXS profile for 5nbv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nbv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5nbv
Deposition date deposition_date2017-03-02
Structure title titleCrystal structure of native alpha-1-antitrypsin with seven stabilising mutations
Keywords keywordsSERPIN, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.66 Å
Radius of gyration Rg (electron density) rg_electron21.31 Å
Forward intensity I(0) i024652100.00
Molecular weight molecular_weight39473.0 kDa
Excluded volume excluded_volume50022 ų
Envelope volume envelope_volume58277 ų
Hydration-shell volume shell_volume22956 ų
Envelope diameter envelope_diameter79.5 Å
Shell Rg shell_rg28.18 Å
Envelope Rg envelope_rg21.73 Å
Shape Rg shape_rg21.29 Å
Total Rg total_rg22.27 Å
Total atoms total_atoms2792
Residues n_residues369
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.3 Å
Rg (real space) rg_real22.64 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real2.4650e+07
I(0) uncertainty (real space) i0_real_error3.0890e+05
Rg (reciprocal space) rg_reciprocal22.64 Å
I(0) (reciprocal space) i0_reciprocal24650000.0000
Solution quality estimate total_estimate0.8681
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.9 Å
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.280
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5980000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.979
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5nbva_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.1 — Serpins

CATH v4.4 (2 domains)

Domain ID domain_id5nbvA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily10 — Antithrombin, subunit I, domain 2
Domain ID domain_id5nbvA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
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8. Citations (1)

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9. Files and Curves (10)