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2beh

Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent antithrombin

Method: X-RAY DIFFRACTION Dmax: 130.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Antithrombin-III

Homo sapiens

UniProt P01008

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain I； UniProt 33–464 Chain L； UniProt 33–464 Mutation：S137A, V317C, T401C 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 4000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.70 Å R-free 0.265

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 2BEH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ANT BIOLOGICAL IMPLICATIONS OF A 3 ANGSTROMS STRUCTURE OF DIMERIC ANTITHROMBIN Deposited 1994-02-28 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 I 33–464（432 aa）
Chain L 33–464（432 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1ATH THE INTACT AND CLEAVED HUMAN ANTITHROMBIN III COMPLEX AS A MODEL FOR SERPIN-PROTEINASE INTERACTIONS Deposited 1993-12-14 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 33–464（432 aa）
Chain B 33–464（432 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å
1AZX ANTITHROMBIN/PENTASACCHARIDE COMPLEX Deposited 1997-11-23 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 L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.90 Å R-free 0.280
1AZX ANTITHROMBIN/PENTASACCHARIDE COMPLEX Deposited 1997-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain I 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.90 Å R-free 0.280
1BR8 IMPLICATIONS FOR FUNCTION AND THERAPY OF A 2.9A STRUCTURE OF BINARY-COMPLEXED ANTITHROMBIN Deposited 1998-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 33–464（432 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；30.6% W/V PEG4000, 35% V/V GLYCEROL, 30 MM CACODYLATE, PH 6.9
Resolution 2.90 Å
1BR8 IMPLICATIONS FOR FUNCTION AND THERAPY OF A 2.9A STRUCTURE OF BINARY-COMPLEXED ANTITHROMBIN Deposited 1998-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 33–464（432 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；30.6% W/V PEG4000, 35% V/V GLYCEROL, 30 MM CACODYLATE, PH 6.9
Resolution 2.90 Å
1BR8 IMPLICATIONS FOR FUNCTION AND THERAPY OF A 2.9A STRUCTURE OF BINARY-COMPLEXED ANTITHROMBIN Deposited 1998-08-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 33–464（432 aa）
Chain L 33–464（432 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；30.6% W/V PEG4000, 35% V/V GLYCEROL, 30 MM CACODYLATE, PH 6.9
Resolution 2.90 Å
1DZG N135Q-S380C-ANTITHROMBIN-III Deposited 2000-02-28 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 L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；5MG/ML 1:1 MIX OF INHIBITORY: LATENT ANTITHROMBIN-III, 10.5% PEG 4000, 65 MM NACACODYLATE, PH 6.5
Resolution 2.80 Å R-free 0.297
1DZG N135Q-S380C-ANTITHROMBIN-III Deposited 2000-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain I 33–464（432 aa）
Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；5MG/ML 1:1 MIX OF INHIBITORY: LATENT ANTITHROMBIN-III, 10.5% PEG 4000, 65 MM NACACODYLATE, PH 6.5
Resolution 2.80 Å R-free 0.297
1DZH P14-FLUORESCEIN-N135Q-S380C-ANTITHROMBIN-III Deposited 2000-02-28 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 L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；5MG/ML 1:1 MIX OF INHIBITORY: LATENT ANTITHROMBIN-III, 10.5% PEG 4000, 65 MM NACACODYLATE, PH 6.5
Resolution 2.85 Å R-free 0.258
1DZH P14-FLUORESCEIN-N135Q-S380C-ANTITHROMBIN-III Deposited 2000-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain I 33–464（432 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；5MG/ML 1:1 MIX OF INHIBITORY: LATENT ANTITHROMBIN-III, 10.5% PEG 4000, 65 MM NACACODYLATE, PH 6.5
Resolution 2.85 Å R-free 0.258
1E03 PLASMA ALPHA ANTITHROMBIN-III AND PENTASACCHARIDE Deposited 2000-03-09 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 L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；5MG/ML 1:1 MIX OF INHIBITORY: LATENT ANTITHROMBIN-III 16% PEG 4000, 63 MM NACACODYLATE PH 7.0, 0.05% AZIDE
Resolution 2.90 Å R-free 0.252
1E03 PLASMA ALPHA ANTITHROMBIN-III AND PENTASACCHARIDE Deposited 2000-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain I 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；5MG/ML 1:1 MIX OF INHIBITORY: LATENT ANTITHROMBIN-III 16% PEG 4000, 63 MM NACACODYLATE PH 7.0, 0.05% AZIDE
Resolution 2.90 Å R-free 0.252
1E04 PLASMA BETA ANTITHROMBIN-III Deposited 2000-03-09 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 I 33–464（432 aa）
Not recorded MAN alpha-D-mannopyranose × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；20MG/ML INHIBITORY ANTITHROMBIN-III IN 20MM TRIS HCL PH 7.4 CRYSTALLIZED IN 16% PEG 4000, 50 MM NA/K PHOSPHATE PH 6.7
Resolution 2.60 Å R-free 0.243
1E04 PLASMA BETA ANTITHROMBIN-III Deposited 2000-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain L 33–464（432 aa）
Not recorded GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；20MG/ML INHIBITORY ANTITHROMBIN-III IN 20MM TRIS HCL PH 7.4 CRYSTALLIZED IN 16% PEG 4000, 50 MM NA/K PHOSPHATE PH 6.7
Resolution 2.60 Å R-free 0.243
1E05 PLASMA ALPHA ANTITHROMBIN-III Deposited 2000-03-09 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 L 33–464（432 aa）
Not recorded MAN alpha-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；CRYSTALS GROWN IN MICROGRAVITY NASA SPACE SHUTTLE MISSION STS-67 20MG/ML LATENT ANTITHROMBIN-III IN 20MM TRIS HCL PH 8.0 CRYSTALLIZED IN 19% PEG 4000, 50 MM NA/K PHOSPHATE PH 6.7, 0.05% AZIDE
Resolution 2.62 Å R-free 0.256
1E05 PLASMA ALPHA ANTITHROMBIN-III Deposited 2000-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain I 33–464（432 aa）
Not recorded MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；CRYSTALS GROWN IN MICROGRAVITY NASA SPACE SHUTTLE MISSION STS-67 20MG/ML LATENT ANTITHROMBIN-III IN 20MM TRIS HCL PH 8.0 CRYSTALLIZED IN 19% PEG 4000, 50 MM NA/K PHOSPHATE PH 6.7, 0.05% AZIDE
Resolution 2.62 Å R-free 0.256
1JVQ Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive loop peptide, and an exogenous tetrapeptide Deposited 2001-08-31 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 I 33–464（432 aa）
Chain L 33–464（432 aa）
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 3350, ammonium fluoride, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.60 Å R-free 0.258
1LK6 Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide Deposited 2002-04-24 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 I 33–464（432 aa）
Chain L 33–464（432 aa）
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 4000, sodium cacodylate, ammonium fluoride, glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.80 Å R-free 0.266
1NQ9 Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State Deposited 2003-01-21 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 I 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；292 K；PEG 3350, Ammonium Fluoride, Tris, glycerol, 1,8-ANS , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.60 Å R-free 0.250
1NQ9 Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State Deposited 2003-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；292 K；PEG 3350, Ammonium Fluoride, Tris, glycerol, 1,8-ANS , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.60 Å R-free 0.250
1OYH Crystal Structure of P13 Alanine Variant of Antithrombin Deposited 2003-04-04 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 I 33–464（432 aa）
Mutation：E381A, S137A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；Na/K Phosphate, PEG 4000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.62 Å R-free 0.258
1OYH Crystal Structure of P13 Alanine Variant of Antithrombin Deposited 2003-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；Na/K Phosphate, PEG 4000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.62 Å R-free 0.258
1R1L Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide (formyl-norleucine-LF) Deposited 2003-09-24 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 I 33–464（432 aa）
Chain L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 GOL GLYCEROL × 1 FOR FORMYL GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 4000, sodium cacodylate, ammonium fluoride, glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.249
1SR5 ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE Deposited 2004-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GU4 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；291 K；PEG 3350, tri-sodium citrate, pH 8.40, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 3.10 Å R-free 0.278
1T1F Crystal Structure of Native Antithrombin in its Monomeric Form Deposited 2004-04-16 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 33–464（432 aa）
Mutation：S137A; V317C; T401C IOD IODIDE ION × 7 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；Sodium Iodide, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.75 Å R-free 0.239
1T1F Crystal Structure of Native Antithrombin in its Monomeric Form Deposited 2004-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 33–464（432 aa）
Mutation：S137A; V317C; T401C IOD IODIDE ION × 7 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；Sodium Iodide, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.75 Å R-free 0.239
1T1F Crystal Structure of Native Antithrombin in its Monomeric Form Deposited 2004-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 33–464（432 aa）
Mutation：S137A; V317C; T401C IOD IODIDE ION × 7 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；Sodium Iodide, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.75 Å R-free 0.239
1TB6 2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex Deposited 2004-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 33–464（432 aa）
Mutation：S137A,V317C,T401C MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；296 K；PEG 3350, lithium citrate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.50 Å R-free 0.245
2ANT THE 2.6 A STRUCTURE OF ANTITHROMBIN INDICATES A CONFORMATIONAL CHANGE AT THE HEPARIN BINDING SITE Deposited 1997-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 33–464（432 aa）
Not recorded NAA 2-acetamido-2-deoxy-beta-D-allopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；18% PEG 4000 50 MM NA/KPO4 PH 6.7
Resolution 2.60 Å R-free 0.290
2ANT THE 2.6 A STRUCTURE OF ANTITHROMBIN INDICATES A CONFORMATIONAL CHANGE AT THE HEPARIN BINDING SITE Deposited 1997-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 33–464（432 aa）
Not recorded NAA 2-acetamido-2-deoxy-beta-D-allopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；18% PEG 4000 50 MM NA/KPO4 PH 6.7
Resolution 2.60 Å R-free 0.290
2B4X Crystal Structure of Antithrombin-III Deposited 2005-09-27 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 I 37–463（427 aa）
Chain L 37–463（427 aa）
Mutation：Y220L, N135A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；294 K；PEG 4000, Sodium/Potassium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.80 Å R-free 0.283
2B5T 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules Deposited 2005-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 33–464（432 aa）
Mutation：I15M, S137A, V317C, T401C GOL GLYCEROL × 12 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；PEG3350, glycerol, ammonium sulfate, (crystallized with NaCl and tris, but not in cryoprotectant), pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.10 Å R-free 0.247
2B5T 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules Deposited 2005-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 33–464（432 aa）
Mutation：I15M, S137A, V317C, T401C GOL GLYCEROL × 12 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；PEG3350, glycerol, ammonium sulfate, (crystallized with NaCl and tris, but not in cryoprotectant), pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.10 Å R-free 0.247
2GD4 Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex Deposited 2006-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 22–464（443 aa） Fragment：Residues 22-464
Mutation：S137A, E347A, K348A, K350A CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；20% PEG 3350, 200mM Calcium Acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.30 Å R-free 0.298
2GD4 Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex Deposited 2006-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 22–464（443 aa） Fragment：Residues 22-464
Mutation：S137A, E347A, K348A, K350A CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；20% PEG 3350, 200mM Calcium Acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.30 Å R-free 0.298
2HIJ Crystal Structure of P14 Alanine Variant of Antithrombin Deposited 2006-06-29 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 I 33–464（432 aa）
Mutation：S380A, N135A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；293 K；12.75% PEG, 50mM K/NaPO4, pH 6.70, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.249
2HIJ Crystal Structure of P14 Alanine Variant of Antithrombin Deposited 2006-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；293 K；12.75% PEG, 50mM K/NaPO4, pH 6.70, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.249
2ZNH Crystal Structure of a Domain-Swapped Serpin Dimer Deposited 2008-04-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 33–464（432 aa）
Chain B 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；20% PEG3350, 0.2M tri-potassium citrate, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.247
3EVJ Intermediate structure of antithrombin bound to the natural pentasaccharide Deposited 2008-10-13 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 I 33–464（432 aa）
Chain L 33–464（432 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；295 K；200mM NH4F, 20% PEG 3350, pH 7.0, EVAPORATION, temperature 295K
Resolution 3.00 Å R-free 0.289
3KCG Crystal structure of the antithrombin-factor IXa-pentasaccharide complex Deposited 2009-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 33–464（432 aa）
Mutation：S137A CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；0.25M Ammonium sulfate, 19.5% PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.230
4EB1 Hyperstable in-frame insertion variant of antithrombin Deposited 2012-03-23 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 I 33–240（208 aa） Fragment：SEE REMARK 999
Chain I 243–464（222 aa） Fragment：SEE REMARK 999
Mutation：S137A, E210del, L211del, insert VLVLVNTRTS Mutation：S137A, E210del, L211del, insert VLVLVNTRTS NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；295 K；17.0% PEG4000, 50 mM sodium/potassium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.255
4EB1 Hyperstable in-frame insertion variant of antithrombin Deposited 2012-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain L 33–464（432 aa） Fragment：UNP RESIDUES 33-464
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；295 K；17.0% PEG4000, 50 mM sodium/potassium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.255

26 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ANT3_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain I； PDBConstruct 1–432； UniProt 33–464 Author chain L； PDBConstruct 1–432； UniProt 33–464

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 2beh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2beh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2beh
Deposition date deposition_date2005-10-24
Structure title titleCrystal structure of antithrombin variant S137A/V317C/T401C with plasma latent antithrombin
Keywords keywordsantithrombin dimer, BLOOD CLOTTING; BLOOD CLOTTING
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_guinier37.41 Å
Radius of gyration Rg (electron density) rg_electron37.67 Å
Forward intensity I(0) i0120891000.00
Molecular weight molecular_weight90340.0 kDa
Excluded volume excluded_volume113600 ų
Envelope volume envelope_volume138970 ų
Hydration-shell volume shell_volume33640 ų
Envelope diameter envelope_diameter133.7 Å
Shell Rg shell_rg39.09 Å
Envelope Rg envelope_rg37.73 Å
Shape Rg shape_rg37.66 Å
Total Rg total_rg37.80 Å
Total atoms total_atoms6360
Residues n_residues816
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 dmax130.0 Å
Rg (real space) rg_real37.98 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real1.2090e+08
I(0) uncertainty (real space) i0_real_error2.0300e+06
Rg (reciprocal space) rg_reciprocal37.64 Å
I(0) (reciprocal space) i0_reciprocal120800000.0000
Solution quality estimate total_estimate0.7399
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.9 Å
Skewness Skewness skewness0.554
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha60750000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.457; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.517; Smooth: 0.725
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2behi_
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
Domain ID domain_idd2behl_
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 (4 domains)

Domain ID domain_id2behI01
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_id2behI02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
Domain ID domain_id2behL01
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_id2behL02
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)