Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

1MH0
DownloadVisualize
BU of 1mh0 by Molmil
Crystal structure of the anticoagulant slow form of thrombin
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Prothrombin
Authors:Pineda, A.O, Savvides, S, Waksman, G, Di Cera, E.
Deposit date:2002-08-18
Release date:2002-11-08
Last modified:2021-10-27
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Crystal structure of the anticoagulant slow form of thrombin
J.Biol.Chem., 277, 2002
1MKX
DownloadVisualize
BU of 1mkx by Molmil
THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING
Descriptor: ALPHA-THROMBIN, PRETHROMBIN-2
Authors:Malkowski, M.G, Edwards, B.F.P.
Deposit date:1997-03-13
Release date:1997-07-07
Last modified:2024-06-05
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding.
Protein Sci., 6, 1997
7KME
DownloadVisualize
BU of 7kme by Molmil
CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2711.
Descriptor: HIRUGEN, SEL2711, SODIUM ION, ...
Authors:Mochalkin, I, Tulinsky, A.
Deposit date:1999-02-26
Release date:1999-03-09
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structures of thrombin retro-inhibited with SEL2711 and SEL2770 as they relate to factor Xa binding.
Acta Crystallogr.,Sect.D, 55, 1999
6V5T
DownloadVisualize
BU of 6v5t by Molmil
Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan
Descriptor: GLYCEROL, Prothrombin, SULFATE ION
Authors:Ruben, E.A, Chen, Z, Di Cera, E.
Deposit date:2019-12-04
Release date:2020-05-13
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2.
J.Biol.Chem., 295, 2020
6V64
DownloadVisualize
BU of 6v64 by Molmil
Crystal structure of human thrombin bound to ppack with tryptophans replaced by 5-F-tryptophan
Descriptor: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, SODIUM ION, Thrombin heavy chain, ...
Authors:Ruben, E.A, Chen, Z, Di Cera, E.
Deposit date:2019-12-04
Release date:2020-05-13
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.29 Å)
Cite:19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2.
J.Biol.Chem., 295, 2020
7SR9
DownloadVisualize
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
DownloadVisualize
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
8UF7
DownloadVisualize
BU of 8uf7 by Molmil
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
8TQS
DownloadVisualize
BU of 8tqs by Molmil
Complex of human thrombin (S195A) bound to a bivalent inhibitor comprised of DNA Aptamer HD22 conjugated to Dabigatran with a linker.
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, DNA (30-MER), ...
Authors:Krishnaswamy, S, Kumar, S.
Deposit date:2023-08-08
Release date:2024-05-01
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (2.207 Å)
Cite:Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors.
Nat Commun, 15, 2024
7MJ5
DownloadVisualize
BU of 7mj5 by Molmil
complex of human thrombin with XC-43
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Putative secreted salivary protein, SODIUM ION, ...
Authors:Lu, S, Tirloni, L, Andersen, J.F.
Deposit date:2021-04-19
Release date:2021-12-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Identification of a substrate-like cleavage-resistant thrombin inhibitor from the saliva of the flea Xenopsylla cheopis.
J.Biol.Chem., 297, 2021
2SPT
DownloadVisualize
BU of 2spt by Molmil
DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, PROTHROMBIN, STRONTIUM ION
Authors:Tulinsky, A.
Deposit date:1994-02-01
Release date:1994-05-31
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1.
Biochemistry, 33, 1994
5GDS
DownloadVisualize
BU of 5gds by Molmil
HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN:HIRUNORM V COMPLEX
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, ALPHA-THROMBIN, HIRUNORM V
Authors:De Simone, G, Lombardi, A, Galdiero, S, Nastri, F, Della Morte, R, Staiano, N, Pedone, C, Bolognesi, M, Pavone, V.
Deposit date:1997-07-17
Release date:1998-01-21
Last modified:2023-08-09
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex.
Protein Sci., 7, 1998
5GIM
DownloadVisualize
BU of 5gim by Molmil
Crystal structure of thrombin-avathrin complex
Descriptor: C-terminal peptide from Putative uncharacterized protein avahiru, N-terminal peptide from Putative uncharacterized protein avahiru, Thrombin light chain, ...
Authors:Kini, R.M, Koh, C.Y, Iyer, J.K, Swaminathan, K.
Deposit date:2016-06-24
Release date:2017-05-03
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Avathrin: a novel thrombin inhibitor derived from a multicopy precursor in the salivary glands of the ixodid tick, Amblyomma variegatum.
FASEB J., 31, 2017
5Z5W
DownloadVisualize
BU of 5z5w by Molmil
VFR12 in complex with LPS micelles
Descriptor: Peptide from Prothrombin
Authors:Saravanan, R, Schmidtchen, A.
Deposit date:2018-01-21
Release date:2018-03-07
Last modified:2024-05-01
Method:SOLUTION NMR
Cite:Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides.
Nat Commun, 9, 2018
5Z5X
DownloadVisualize
BU of 5z5x by Molmil
HVF18 in complex with LPS micelles
Descriptor: Peptide from Prothrombin
Authors:Saravanan, R, Schmidtchen, A.
Deposit date:2018-01-21
Release date:2018-03-07
Last modified:2024-05-01
Method:SOLUTION NMR
Cite:Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides.
Nat Commun, 9, 2018
5JDU
DownloadVisualize
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
6BJR
DownloadVisualize
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
3B9F
DownloadVisualize
BU of 3b9f by Molmil
1.6 A structure of the PCI-thrombin-heparin complex
Descriptor: 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose, GLYCEROL, Plasma serine protease inhibitor, ...
Authors:Li, W, Adams, T.E, Huntington, J.A.
Deposit date:2007-11-05
Release date:2008-04-22
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.
Proc.Natl.Acad.Sci.Usa, 105, 2008
3B23
DownloadVisualize
BU of 3b23 by Molmil
Crystal structure of thrombin-variegin complex: Insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors
Descriptor: Thrombin heavy chain, Thrombin light chain, Variegin
Authors:Koh, C.Y, Kumar, S, Swaminathan, K, Kini, R.M.
Deposit date:2011-07-20
Release date:2011-11-23
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of thrombin in complex with s-variegin: insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors
Plos One, 6, 2011
3BIV
DownloadVisualize
BU of 3biv by Molmil
Human thrombin-in complex with UB-THR11
Descriptor: (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin, ...
Authors:Gerlach, C, Smolinski, M, Steuber, H, Sotriffer, C.A, Heine, A, Hangauer, D.G, Klebe, G.
Deposit date:2007-12-01
Release date:2007-12-25
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Thermodynamic Inhibition Profile of a Cyclopentyl and a Cyclohexyl Derivative towards Thrombin: The Same but for Different Reasons
Angew.Chem.Int.Ed.Engl., 46, 2007
3LDX
DownloadVisualize
BU of 3ldx by Molmil
Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif
Descriptor: Hirudin variant-1, N-[2-(carbamimidamidooxy)ethyl]-2-{3-[(2,2-difluoro-2-phenylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}acetamide, Thrombin heavy chain, ...
Authors:Spurlino, J.C.
Deposit date:2010-01-13
Release date:2011-08-10
Last modified:2017-07-19
Method:X-RAY DIFFRACTION (2.246 Å)
Cite:Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif
To be Published
5JZY
DownloadVisualize
BU of 5jzy by Molmil
Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3-cyclohexyl-D-alanyl-N-[(4-carbamimidoylphenyl)methyl]-L-prolinamide, DIMETHYL SULFOXIDE, ...
Authors:Sandner, A, Heine, A, Klebe, G.
Deposit date:2016-05-17
Release date:2017-06-07
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (1.27 Å)
Cite:Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
J.Med.Chem., 62, 2019
5NHU
DownloadVisualize
BU of 5nhu by Molmil
HUMAN ALPHA THROMBIN COMPLEXED WITH ANOPHELES GAMBIAE cE5 ANTICOAGULANT
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, AGAP008004-PA, Prothrombin, ...
Authors:Ripoll-Rozada, J, Pereira, P.J.B.
Deposit date:2017-03-22
Release date:2017-06-14
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Functional analyses yield detailed insight into the mechanism of thrombin inhibition by the antihemostatic salivary protein cE5 from Anopheles gambiae.
J. Biol. Chem., 292, 2017
3BV9
DownloadVisualize
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
3LU9
DownloadVisualize
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

221371

数据于2024-06-19公开中

PDB statisticsPDBj update infoContact PDBjnumon