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- PDB-1mkw: THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mkw | ||||||
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Title | THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING | ||||||
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![]() | COMPLEX (BLOOD COAGULATION/PROENZYME) / COMPLEX (BLOOD COAGULATION-PROENZYME) / THROMBIN / PRETHROMBIN-2 / PLASMA / SERINE PROTEASE / COMPLEX (BLOOD COAGULATION-PROENZYME) complex | ||||||
Function / homology | ![]() fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Malkowski, M.G. / Edwards, B.F.P. | ||||||
![]() | ![]() Title: 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. Authors: Malkowski, M.G. / Martin, P.D. / Guzik, J.C. / Edwards, B.F. #1: ![]() Title: Bovine Thrombin Complexed with an Uncleavable Analog of Residues 7-19 of Fibrinogen a Alpha: Geometry of the Catalytic Triad and Interactions of the P1', P2', and P3' Substrate Residues Authors: Martin, P.D. / Malkowski, M.G. / Dimaio, J. / Konishi, Y. / Ni, F. / Edwards, B.F. #2: ![]() Title: The Isomorphous Structures of Prethrombin2, Hirugen-, and Ppack-Thrombin: Changes Accompanying Activation and Exosite Binding to Thrombin Authors: Vijayalakshmi, J. / Padmanabhan, K.P. / Mann, K.G. / Tulinsky, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.5 KB | Display | ![]() |
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PDB format | ![]() | 103.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.4 KB | Display | ![]() |
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Full document | ![]() | 427.9 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THERE ARE TWO INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS ALPHA THROMBIN, AND COMPLEX II IS PRETHROMBIN-2. ALPHA THROMBIN IN COMPLEX I HAS BEEN ASSIGNED CHAIN INDICATORS *L* AND *H*, AND PRETHROMBIN-2 IN COMPLEX II HAS BEEN ASSIGNED CHAIN INDICATOR *K*. |
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Components
#1: Protein/peptide | Mass: 5735.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 35489.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Water | ChemComp-HOH / |
Sequence details | CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 24% POLYETHYLENE GLYCOL 2000, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→7 Å / Num. obs: 44681 / % possible obs: 79 % / Observed criterion σ(I): 0 / Rsym value: 0.072 |
Reflection | *PLUS Num. measured all: 90801 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.5 Å / % possible obs: 57 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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