1oyh

Crystal Structure of P13 Alanine Variant of Antithrombin

Method: X-RAY DIFFRACTION D_max: 130.6 Å Quality: GOOD

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

Antithrombin-III

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	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 33–464	Mutation：E381A, S137A	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	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
2	Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain L； UniProt 33–464	Mutation：E381A, S137A	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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	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

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 1OYH	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 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 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 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 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 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 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 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 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 construct 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 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 mutation/modification 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）	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 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 mutation/modification 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）	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 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 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 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 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 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 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 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 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 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 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 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 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
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 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 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 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 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 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 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 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 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 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 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 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
2BEH Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent antithrombin Deposited 2005-10-24	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 33–464（432 aa） Chain L 33–464（432 aa）	Mutation：S137A, V317C, T401C	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
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 mutation/modification 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 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 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 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 construct Different mutation/modification Different oligomeric state 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 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 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 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 42 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

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	1oyh
Deposition date deposition_date	2003-04-04
Structure title title	Crystal Structure of P13 Alanine Variant of Antithrombin
Keywords keywords	thrombin; inhibition; heparin analogue; SERINE PROTEASE INHIBITOR, BLOOD CLOTTING; BLOOD CLOTTING
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	37.89 Å
Radius of gyration Rg (electron density) rg_electron	38.05 Å
Forward intensity I(0) i0	131209000.00
Molecular weight molecular_weight	93915.0 kDa
Excluded volume excluded_volume	118070 Å³
Envelope volume envelope_volume	150060 Å³
Hydration-shell volume shell_volume	35674 Å³
Envelope diameter envelope_diameter	133.3 Å
Shell Rg shell_rg	39.87 Å
Envelope Rg envelope_rg	37.92 Å
Shape Rg shape_rg	38.03 Å
Total Rg total_rg	38.23 Å
Total atoms total_atoms	6607
Residues n_residues	826
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	130.6 Å
Rg (real space) rg_real	38.44 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	1.3120e+08
I(0) uncertainty (real space) i0_real_error	2.3110e+06
Rg (reciprocal space) rg_reciprocal	38.11 Å
I(0) (reciprocal space) i0_reciprocal	131200000.0000
Solution quality estimate total_estimate	0.7536
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.538
Kurtosis Kurtosis kurtosis	-0.567
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	64570000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.505; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.592; Smooth: 0.687

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Antithrombin-III
Molecular weight formula_weight	49027.0 kDa
Mutation mutation	E381A, S137A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I
Atom count atom_count	6661

HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYVSDAFHKAFLEVNEEGSAAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Antithrombin-III
Molecular weight formula_weight	49101.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	54

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1oyhi_
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

Domain ID domain_id	d1oyhl_
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 (4 domains)

Domain ID domain_id	1oyhI01
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

Domain ID domain_id	1oyhI02
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	1oyhL01
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

Domain ID domain_id	1oyhL02
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

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8. Citations (1)

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Unit-cell length a length_a	68.998 Å
Unit-cell length b length_b	98.573 Å
Unit-cell length c length_c	89.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	39.000 Å
R factor r_factor	—
R_work r_work	0.2210
R_free r_free	0.2580

fit	/app/data/saxs_computation/oy/1oyh/1oyh.fit
pddf	/app/data/pr_computation/oy/1oyh/1oyh.pr.out
profile	/app/data/saxs_computation/oy/1oyh/1oyh.dat

Crystal Structure of P13 Alanine Variant of Antithrombin

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

Antithrombin-III

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)