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- PDB-2spt: DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2spt | ||||||
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Title | DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1 | ||||||
![]() | PROTHROMBIN | ||||||
![]() | HYDROLASE(SERINE PROTEINASE) | ||||||
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 | ![]() | ||||||
![]() | Tulinsky, A. | ||||||
![]() | ![]() Title: Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1. Authors: Seshadri, T.P. / Skrzypczak-Jankun, E. / Yin, M. / Tulinsky, A. #1: ![]() Title: The Ca2+ Ion and Membrane Binding Structure of the Gla Domain of Ca-Prothrombin Fragment 1 Authors: Soriano-Garcia, M. / Padmanabhan, K. / De Vos, A.M. / Tulinsky, A. #2: ![]() Title: Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.5 KB | Display | ![]() |
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PDB format | ![]() | 33.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 54 / 2: CIS PROLINE - PRO 95 |
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Components
#1: Protein | Mass: 16729.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Sugar | ChemComp-NAG / | ||||
#3: Chemical | ChemComp-SR / #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.77 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging dropDetails: taken from Soriano-Garacia, M. et al (1989), Biochemistry, 28, 6805-6810. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Num. all: 10366 / Num. obs: 5331 |
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Processing
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Refinement | Resolution: 2.5→7 Å /
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Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |