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- PDB-1hcg: STRUCTURE OF HUMAN DES(1-45) FACTOR XA AT 2.2 ANGSTROMS RESOLUTION -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hcg | ||||||
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Title | STRUCTURE OF HUMAN DES(1-45) FACTOR XA AT 2.2 ANGSTROMS RESOLUTION | ||||||
![]() | (BLOOD COAGULATION FACTOR XA) x 2 | ||||||
![]() | COAGULATION FACTOR | ||||||
Function / homology | ![]() coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Tulinsky, A. / Padmanabhan, K. | ||||||
![]() | ![]() Title: Structure of human des(1-45) factor Xa at 2.2 A resolution. Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W. #1: ![]() Title: Three-Dimensional Structure of the Apo Form of the N-Terminal Egf-Like Module of Blood Coagulation Factor X as Determined by NMR Spectroscopy and Simulated Folding Authors: Ullner, M. / Selander, M. / Persson, E. / Stenflo, J. / Drakenberg, T. / Teleman, O. #2: ![]() Title: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M. #3: ![]() Title: Comparative Model-Building of the Mammalian Serine Proteases Authors: Greer, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 55.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.9 KB | Display | ![]() |
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Full document | ![]() | 411.4 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: RESIDUES LEU A 247 AND GLN B 10 HAVE RAMACHANDRAN ANGLES OUTSIDE THE ALLOWED REGION. THESE RESIDUES ARE VERY WELL-DEFINED IN THE ELECTRON DENSITY. |
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Components
#1: Protein | Mass: 27201.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Protein | Mass: 5504.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.24 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 17121 / % possible obs: 61.5 % / Observed criterion σ(F): 2 / Num. measured all: 53755 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.5 Å / % possible obs: 38 % |
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Processing
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Refinement | Resolution: 2.2→7 Å / σ(F): 4 Details: SOME OF THE WATERS WHICH ARE MORE THAN 4 ANGSTROMS FROM THE PROTEIN MAY BE PART OF THE FLEXIBLY DISORDERED N-TERMINAL EGF-LIKE DOMAIN. RESIDUES LEU A 247 AND GLN B 10 HAVE RAMACHANDRAN ...Details: SOME OF THE WATERS WHICH ARE MORE THAN 4 ANGSTROMS FROM THE PROTEIN MAY BE PART OF THE FLEXIBLY DISORDERED N-TERMINAL EGF-LIKE DOMAIN. RESIDUES LEU A 247 AND GLN B 10 HAVE RAMACHANDRAN ANGLES OUTSIDE THE ALLOWED REGION. THESE RESIDUES ARE VERY WELL-DEFINED IN THE ELECTRON DENSITY.
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Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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