4RN6
| Structure of prethrombin-2 mutant s195a bound to the active site inhibitor argatroban | Descriptor: | (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid, Thrombin heavy chain | Authors: | Pozzi, N, Chen, Z, Zapata, F, Niu, W, Barranco-Medina, S, Pelc, L.A, Di Cera, E. | Deposit date: | 2014-10-23 | Release date: | 2014-11-05 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Autoactivation of thrombin precursors. J.Biol.Chem., 288, 2013
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5EDK
| Crystal structure of prothrombin deletion mutant residues 146-167 ( Form II ). | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Pozzi, N, Chen, Z, Di Cera, E. | Deposit date: | 2015-10-21 | Release date: | 2016-01-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (3.214 Å) | Cite: | How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J.Biol.Chem., 291, 2016
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4DT7
| Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C | Descriptor: | ACETATE ION, DI(HYDROXYETHYL)ETHER, SODIUM ION, ... | Authors: | Pozzi, N, Barranco-Medina, S, Chen, Z, Di Cera, E. | Deposit date: | 2012-02-20 | Release date: | 2012-05-09 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Exposure of R169 controls protein C activation and autoactivation. Blood, 120, 2012
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5EDM
| Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I ) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | Authors: | Pozzi, N, Chen, Z, Di Cera, E. | Deposit date: | 2015-10-21 | Release date: | 2016-01-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J.Biol.Chem., 291, 2016
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5JDU
| Crystal structure for human thrombin mutant D189A | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, GLYCEROL, ... | Authors: | Pozzi, N, Chen, Z, Di Cera, E. | Deposit date: | 2016-04-17 | Release date: | 2016-07-13 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin. Biochemistry, 55, 2016
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3SQE
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3SQH
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4HFP
| Structure of thrombin mutant S195a bound to the active site inhibitor argatroban | Descriptor: | (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid, Prothrombin, SODIUM ION | Authors: | Pozzi, N, Chen, Z, Zapata, F, Lin, W, Barranco-Medina, S, Pelc, L.A, Di Cera, E. | Deposit date: | 2012-10-05 | Release date: | 2013-03-13 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Autoactivation of thrombin precursors. J.Biol.Chem., 288, 2013
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4HZH
| Structure of recombinant Gla-domainless prothrombin mutant S525A | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Prothrombin | Authors: | Pozzi, N, Niu, W, Gohara, D.W, Chen, Z, Di Cera, E. | Deposit date: | 2012-11-15 | Release date: | 2013-06-26 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Crystal structure of prothrombin reveals conformational flexibility and mechanism of activation. J.Biol.Chem., 288, 2013
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4H6T
| Crystal structure of prethrombin-2 mutant E14eA/D14lA/E18A/S195A | Descriptor: | PHOSPHATE ION, Prothrombin | Authors: | Pozzi, N, Chen, Z, Zapata, F, Pelc, L.A, Di Cera, E. | Deposit date: | 2012-09-19 | Release date: | 2013-03-13 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Autoactivation of thrombin precursors. J.Biol.Chem., 288, 2013
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4H6S
| Crystal structure of thrombin mutant E14eA/D14lA/E18A/S195A | Descriptor: | Prothrombin, SODIUM ION | Authors: | Pozzi, N, Chen, Z, Zapata, F, Pelc, L.A, Di Cera, E. | Deposit date: | 2012-09-19 | Release date: | 2013-03-13 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.19 Å) | Cite: | Autoactivation of thrombin precursors. J.Biol.Chem., 288, 2013
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3R3G
| Structure of human thrombin with residues 145-150 of murine thrombin. | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, SODIUM ION, Thrombin Heavy Chain, ... | Authors: | Pozzi, N, Chen, R, Chen, Z, Bah, A, Di Cera, E. | Deposit date: | 2011-03-15 | Release date: | 2011-05-11 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Rigidification of the autolysis loop enhances Na(+) binding to thrombin. Biophys.Chem., 159, 2011
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4NZQ
| Crystal structure of Ca2+-free prothrombin deletion mutant residues 146-167 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Prothrombin | Authors: | Pozzi, N, Chen, Z, Shropshire, D.B, Pelc, L.A, Di Cera, E. | Deposit date: | 2013-12-12 | Release date: | 2014-05-21 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (2.807 Å) | Cite: | The linker connecting the two kringles plays a key role in prothrombin activation. Proc.Natl.Acad.Sci.USA, 111, 2014
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4O03
| Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Prothrombin | Authors: | Pozzi, N, Chen, Z, Shropshire, D.B, Pelc, L.A, Di Cera, E. | Deposit date: | 2013-12-13 | Release date: | 2014-05-21 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (3.38 Å) | Cite: | The linker connecting the two kringles plays a key role in prothrombin activation. Proc.Natl.Acad.Sci.USA, 111, 2014
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6BJR
| Crystal structure of prothrombin mutant S101C/A470C | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, Prothrombin, ... | Authors: | Chinnaraj, M, Chen, Z, Pelc, L, Grese, Z, Bystranowska, D, Di Cera, E, Pozzi, N. | Deposit date: | 2017-11-06 | Release date: | 2018-06-27 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (6 Å) | Cite: | Structure of prothrombin in the closed form reveals new details on the mechanism of activation. Sci Rep, 8, 2018
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8UF7
| Cryo-EM structure of POmAb, a Type-I anti-prothrombin antiphospholipid antibody, bound to kringle-1 of human prothrombin | Descriptor: | POmAb Heavy Chain, POmAb Light Chain, Prothrombin | Authors: | Kumar, S, Summers, B, Basore, K, Pozzi, N. | Deposit date: | 2023-10-03 | Release date: | 2024-02-14 | Last modified: | 2024-05-22 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Cryo-EM structure and functional basis of prothrombin recognition by a type I antiprothrombin antiphospholipid antibody. Blood, 143, 2024
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6C2W
| Crystal structure of human prothrombin mutant S101C/A470C | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, Prothrombin, ... | Authors: | Chinnaraj, M, Chen, Z, Pelc, L, Grese, Z, Bystranowska, D, Di Cera, E, Pozzi, N. | Deposit date: | 2018-01-09 | Release date: | 2018-02-28 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (4.12 Å) | Cite: | Structure of prothrombin in the closed form reveals new details on the mechanism of activation. Sci Rep, 8, 2018
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5TO3
| Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, ... | Authors: | Barranco-Medina, S, Murphy, M, Pelc, L, Chen, Z, Di Cera, E, Pozzi, N. | Deposit date: | 2016-10-16 | Release date: | 2017-03-29 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | Rational Design of Protein C Activators. Sci Rep, 7, 2017
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4RKJ
| Crystal structure of thrombin mutant S195T (free form) | Descriptor: | GLYCEROL, POTASSIUM ION, Thrombin heavy chain, ... | Authors: | Pelc, A.L, Chen, Z, Gohara, D.W, Vogt, A.D, Pozzi, N, Di Cera, E. | Deposit date: | 2014-10-13 | Release date: | 2015-03-11 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Why ser and not thr brokers catalysis in the trypsin fold. Biochemistry, 54, 2015
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4RKO
| Crystal structure of thrombin mutant S195T bound with PPACK | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, ... | Authors: | Pelc, A.L, Chen, Z, Gohara, D.W, Vogt, A.D, Pozzi, N, Di Cera, E. | Deposit date: | 2014-10-13 | Release date: | 2015-03-11 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Why ser and not thr brokers catalysis in the trypsin fold. Biochemistry, 54, 2015
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3S7H
| Structure of thrombin mutant Y225P in the E* form | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Prothrombin | Authors: | Niu, W, Chen, Z, Gandhi, P, Vogt, A, Pozzi, N, Pele, L.A, Zapata, F, Di Cera, E. | Deposit date: | 2011-05-26 | Release date: | 2011-07-06 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystallographic and Kinetic Evidence of Allostery in a Trypsin-like Protease. Biochemistry, 50, 2011
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3S7K
| Structure of thrombin mutant Y225P in the E form | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, POTASSIUM ION, Prothrombin | Authors: | Niu, W, Chen, Z, Gandhi, P, Vogt, A, Pozzi, N, Pele, L.A, Zapata, F, Di Cera, E. | Deposit date: | 2011-05-26 | Release date: | 2011-07-06 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystallographic and Kinetic Evidence of Allostery in a Trypsin-like Protease. Biochemistry, 50, 2011
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6V06
| Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-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, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Beta-2-glycoprotein 1, ... | Authors: | Chen, Z, Ruben, E.A, Planer, W, Chinnaraj, M, Zuo, X, Pengo, V, Macor, P, Tedesco, F, Pozzi, N. | Deposit date: | 2019-11-18 | Release date: | 2020-06-17 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | The J-elongated conformation of beta2-glycoprotein I predominates in solution: implications for our understanding of antiphospholipid syndrome. J.Biol.Chem., 295, 2020
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6V09
| Crystal structure of human recombinant Beta-2 glycoprotein I short tag (ST-B2GPI) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-2-glycoprotein 1, SULFATE ION, ... | Authors: | Chen, Z, Ruben, E.A, Planer, W, Chinnaraj, M, Zuo, X, Pengo, V, Macor, P, Tedesco, F, Pozzi, N. | Deposit date: | 2019-11-18 | Release date: | 2020-06-17 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.99 Å) | Cite: | The J-elongated conformation of beta2-glycoprotein I predominates in solution: implications for our understanding of antiphospholipid syndrome. J.Biol.Chem., 295, 2020
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6V08
| Crystal structure of human recombinant Beta-2 glycoprotein I (hrB2GPI) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-2-glycoprotein 1, SULFATE ION, ... | Authors: | Chen, Z, Ruben, E.A, Planer, W, Chinnaraj, M, Zuo, X, Pengo, V, Macor, P, Tedesco, F, Pozzi, N. | Deposit date: | 2019-11-18 | Release date: | 2020-06-17 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.58 Å) | Cite: | The J-elongated conformation of beta2-glycoprotein I predominates in solution: implications for our understanding of antiphospholipid syndrome. J.Biol.Chem., 295, 2020
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