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7SR9
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BU of 7sr9 by Molmil
Human alpha-thrombin with 180- and 220- loops replaced with homologous loops from protein C
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SULFATE ION, ...
Authors:Di Cera, E, Ruben, E.A, Chen, Z.
Deposit date:2021-11-08
Release date:2021-12-08
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The active site region plays a critical role in Na + binding to thrombin.
J.Biol.Chem., 298, 2022
7TPP
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BU of 7tpp by Molmil
Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution
Descriptor: Activated factor Xa heavy chain, Coagulation factor Va, Factor X light chain, ...
Authors:Di Cera, E, Ruben, E.A.
Deposit date:2022-01-25
Release date:2022-05-04
Last modified:2022-06-29
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:Cryo-EM structure of the prothrombin-prothrombinase complex.
Blood, 139, 2022
9CTH
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BU of 9cth by Molmil
Preliminary map of the Prothrombin-prothrombinase complex on nano discs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Activated Factor V (FVa) heavy chain, Activated Factor V (FVa) light chain, ...
Authors:Stojanovski, B.M, Mohammed, B.M, Di Cera, E.
Deposit date:2024-07-25
Release date:2024-08-07
Last modified:2024-08-14
Method:ELECTRON MICROSCOPY (6.47 Å)
Cite:The Prothrombin-Prothrombinase Interaction.
Subcell Biochem, 104, 2024
6P9U
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BU of 6p9u by Molmil
Crystal structure of human thrombin mutant W215A
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Prothrombin, ZINC ION
Authors:Pelc, L.A, Koester, S.K, Chen, Z, Di Cera, E.
Deposit date:2019-06-10
Release date:2019-09-04
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin.
Sci Rep, 9, 2019
2A0Q
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BU of 2a0q by Molmil
Structure of thrombin in 400 mM potassium chloride
Descriptor: 2-acetamido-2-deoxy-alpha-D-glucopyranose, CHLORIDE ION, POTASSIUM ION, ...
Authors:Papaconstantinou, M, Carrell, C.J, Pineda, A.O, Bobofchak, K.M, Mathews, F.S, Flordellis, C.S, Maragoudakis, M.E, Tsopanoglou, N.E, di Cera, E.
Deposit date:2005-06-16
Release date:2005-07-12
Last modified:2021-10-20
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Thrombin Functions through Its RGD Sequence in a Non-canonical Conformation.
J.Biol.Chem., 280, 2005
3LU9
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BU of 3lu9 by Molmil
Crystal structure of human thrombin mutant S195A in complex with the extracellular fragment of human PAR1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Proteinase-activated receptor 1, ...
Authors:Gandhi, P.S, Chen, Z, Di Cera, E.
Deposit date:2010-02-17
Release date:2010-03-16
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure of thrombin bound to the uncleaved extracellular fragment of PAR1.
J.Biol.Chem., 285, 2010
4DT7
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BU of 4dt7 by Molmil
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
8TN9
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BU of 8tn9 by Molmil
Structural architecture of the acidic region of the B domain of coagulation factor V
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Coagulation factor V
Authors:Mohammed, B.M, Basore, K, Summers, B, Pelc, L.A, Di Cera, E.
Deposit date:2023-08-01
Release date:2023-10-04
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (3.05 Å)
Cite:Structural architecture of the acidic region of the B domain of coagulation factor V.
J.Thromb.Haemost., 22, 2024
3BEF
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BU of 3bef by Molmil
Crystal structure of thrombin bound to the extracellular fragment of PAR1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Proteinase-activated receptor 1, Prothrombin
Authors:Gandhi, P.S, Bah, A, Chen, Z, Mathews, F.S, Di Cera, E.
Deposit date:2007-11-17
Release date:2008-01-01
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural identification of the pathway of long-range communication in an allosteric enzyme.
Proc.Natl.Acad.Sci.Usa, 105, 2008
6BJR
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BU of 6bjr by Molmil
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
1B7X
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BU of 1b7x by Molmil
STRUCTURE OF HUMAN ALPHA-THROMBIN Y225I MUTANT BOUND TO D-PHE-PRO-ARG-CHLOROMETHYLKETONE
Descriptor: PROTEIN (INHIBITOR), PROTEIN (THROMBIN HEAVY CHAIN), PROTEIN (THROMBIN LIGHT CHAIN)
Authors:Caccia, S, Futterer, K, Di Cera, E, Waksman, G.
Deposit date:1999-01-25
Release date:1999-03-02
Last modified:2023-08-09
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Unexpected crucial role of residue 225 in serine proteases.
Proc.Natl.Acad.Sci.USA, 96, 1999
6C2W
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BU of 6c2w by Molmil
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
5JDU
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BU of 5jdu by Molmil
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
2PV9
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BU of 2pv9 by Molmil
Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Proteinase-activated receptor 4, Thrombin heavy chain, ...
Authors:Bah, A, Chen, Z, Bush-Pelc, L.A, Mathews, F.S, Di Cera, E.
Deposit date:2007-05-09
Release date:2007-07-10
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.
Proc.Natl.Acad.Sci.Usa, 104, 2007
2PUX
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BU of 2pux by Molmil
Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Proteinase-activated receptor 3, Thrombin heavy chain, ...
Authors:Bah, A, Chen, Z, Bush-Pelc, L.A, Mathews, F.S, Di Cera, E.
Deposit date:2007-05-09
Release date:2007-07-10
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.
Proc.Natl.Acad.Sci.Usa, 104, 2007
5EDK
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BU of 5edk by Molmil
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
8FDG
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BU of 8fdg by Molmil
Cryo-EM structure of coagulation factor V short
Descriptor: Coagulation factor V
Authors:Mohammed, B.M, Pelc, L.A, Rau, M.J, Di Cera, E.
Deposit date:2022-12-03
Release date:2023-03-15
Last modified:2023-07-12
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Cryo-EM structure of coagulation factor V short.
Blood, 141, 2023
2FMJ
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BU of 2fmj by Molmil
220-loop mutant of streptomyces griseus trypsin
Descriptor: CALCIUM ION, SULFATE ION, Trypsin
Authors:Page, M.J, Di Cera, E.
Deposit date:2006-01-09
Release date:2006-05-23
Last modified:2021-10-20
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Conversion of trypsin into a Na(+)-activated enzyme.
Biochemistry, 45, 2006
4RKJ
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BU of 4rkj by Molmil
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
4RKO
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BU of 4rko by Molmil
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
4RN6
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BU of 4rn6 by Molmil
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
3BEI
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BU of 3bei by Molmil
Crystal structure of the slow form of thrombin in a self_inhibited conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Prothrombin
Authors:Gandhi, P.S, Chen, Z, Mathews, F.S, Di Cera, E.
Deposit date:2007-11-19
Release date:2007-12-25
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Structural identification of the pathway of long-range communication in an allosteric enzyme.
Proc.Natl.Acad.Sci.Usa, 105, 2008
3BV9
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BU of 3bv9 by Molmil
Structure of Thrombin Bound to the Inhibitor FM19
Descriptor: FM19 inhibitor, GLYCEROL, IODIDE ION, ...
Authors:Nieman, M.T, Burke, F, Warnock, M, Zhou, Y, Sweigert, J, Chen, A, Ricketts, D, Lucchesi, B.R, Chen, Z, Di Cera, E, Hilfinger, J, Mosberg, H.I, Schmaier, A.H.
Deposit date:2008-01-05
Release date:2008-03-04
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Thrombostatin FM compounds: direct thrombin inhibitors - mechanism of action in vitro and in vivo.
J.Thromb.Haemost., 6, 2008
4NZQ
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BU of 4nzq by Molmil
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
3MVT
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BU of 3mvt by Molmil
Crystal structure of apo mADA at 2.2A resolution
Descriptor: Adenosine deaminase, CHLORIDE ION, GLYCEROL
Authors:Niu, W, Shu, Q, Chen, Z, Mathews, S, Di Cera, E, Frieden, C.
Deposit date:2010-05-04
Release date:2010-10-13
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:The role of Zn2+ on the structure and stability of murine adenosine deaminase.
J.Phys.Chem.B, 114, 2010

 

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