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Yorodumi- PDB-1dva: Crystal Structure of the Complex Between the Peptide Exosite Inhi... -
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-Basic information
Entry | Database: PDB / ID: 1dva | |||||||||
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Title | Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / protein-peptide complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | |||||||||
Authors | Eigenbrot, C. / Ultsch, M.H. | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Peptide exosite inhibitors of factor VIIa as anticoagulants. Authors: Dennis, M.S. / Eigenbrot, C. / Skelton, N.J. / Ultsch, M.H. / Santell, L. / Dwyer, M.A. / O'Connell, M.P. / Lazarus, R.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dva.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dva.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dva_validation.pdf.gz | 673 KB | Display | wwPDB validaton report |
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Full document | 1dva_full_validation.pdf.gz | 723.4 KB | Display | |
Data in XML | 1dva_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 1dva_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dva ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dva | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-DES-GLA FACTOR VIIA ... , 2 types, 4 molecules HILM
#1: Protein | Mass: 28103.256 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PCMV5 / Cell line (production host): HUMAN KIDNEY CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa #2: Protein | Mass: 10994.179 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PCMV5 / Cell line (production host): HUMAN KIDNEY CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa |
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-Protein/peptide , 1 types, 2 molecules XY
#3: Protein/peptide | Mass: 2198.461 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Peptide E-76 was synthesized on a solid support, then cleaved and purified |
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-Sugars , 4 types, 5 molecules
#4: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose | ||||
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#8: Sugar | #9: Sugar | ChemComp-GLC / | #10: Sugar | ChemComp-FUL / | |
-Non-polymers , 4 types, 12 molecules
#5: Chemical | #6: Chemical | ChemComp-CA / #7: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE- ...THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETH |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % | ||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG4000, t-butanol, sodium cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 16915 / Num. obs: 16915 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2478 / % possible all: 98.4 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Resolution: 3→50 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL WAS APPLIED THERE IS UNPUBLISHED EXPERIMENTAL EVIDENCE THAT THE CARBOHYDRATE ATTACHED TO CHAINS L AND M DIFFERS FROM THAT DESCRIBED IN THIS ENTRY. SER 52 CARRIES 2 OR 3 ...Details: BULK SOLVENT MODEL WAS APPLIED THERE IS UNPUBLISHED EXPERIMENTAL EVIDENCE THAT THE CARBOHYDRATE ATTACHED TO CHAINS L AND M DIFFERS FROM THAT DESCRIBED IN THIS ENTRY. SER 52 CARRIES 2 OR 3 GLUCOSE RESIDUES, AND SER 60 CARRIES ALPHA-L-FUCOSE. THE ELECTRON DENSITY IN THIS REGION IS IMPERFECT, AND WAS FIT WITHOUT THIS INFORMATION. THE FIT IS ONLY MODERATELY SUCCESFUL.
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Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1 / Weight position: 200
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0.2 / % reflection Rfree: 3.9 % / Rfactor obs: 0.225 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.361 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.35 |