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- PDB-1c1v: RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c1v | |||||||||
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Title | RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / ZN(II)-MEDIATED SERINE PROTEASE INHIBITORS / PH DEPENDENCE / ZN(II) AFFINITY STUCTURE-BASED DRUG DESIGN / SERINE PROTEASE/INHIBITOR / ![]() | |||||||||
Function / homology | ![]() positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Katz, B.A. / Luong, C. | |||||||||
![]() | ![]() Title: Design of potent selective zinc-mediated serine protease inhibitors. Authors: Katz, B.A. / Clark, J.M. / Finer-Moore, J.S. / Jenkins, T.E. / Johnson, C.R. / Ross, M.J. / Luong, C. / Moore, W.R. / Stroud, R.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.6 KB | Display | ![]() |
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PDB format | ![]() | 118.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1c1nC ![]() 1c1oC ![]() 1c1pC ![]() 1c1qC ![]() 1c1rC ![]() 1c1tC ![]() 1c1uC ![]() 1c1wC ![]() 1c2dC ![]() 1c2eC ![]() 1c2fC ![]() 1c2gC ![]() 1c2hC ![]() 1c2iC ![]() 1c2jC ![]() 1c2kC ![]() 1c2lC ![]() 1c2mC ![]() 1xufC ![]() 1xugC ![]() 1xuhC ![]() 1xuiC ![]() 1xujC ![]() 1xukC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein/peptide , 2 types, 2 molecules LI
#1: Protein/peptide | ![]() Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#3: Protein/peptide | ![]() Mass: 1491.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules H
#2: Protein | ![]() Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 267 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BAB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BAB.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-BAB / | #7: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | HIS_H57 IS MONOPROTONATED ON THE DELTA NITROGEN. HIS_H91 AND HIS_H119 ARE MONOPROTONATED ON THE ...HIS_H57 IS MONOPROTON |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.51 % |
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Crystal grow![]() | pH: 7 Details: THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM ...Details: THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C. GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 (AMICON) TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-BABIM-ZN+2 WERE GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5 MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION (0.10 M TRIS, 0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 7.00). A CO-CRYSTAL WAS SOAKED IN 30 % PEG 4K,0.50 M NACL, 0.10 M TRIS, 46 MM ZN+2, PH 7.00, SATURATED IN BABIM AND CONTAINING 2 % DMSO. |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MSC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.98→44.42 Å / Num. obs: 22211 / % possible obs: 62 % / Observed criterion σ(I): 1 / Redundancy: 1.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.98→2.07 Å / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 1.8 / % possible all: 36.3 |
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Processing
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Refinement | Method to determine structure![]() Resolution: 1.98→7.5 Å / Cross valid method: X-PLOR / σ(F): 2.75 Details: BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X-PLOR SCRIPT.
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Refinement step | Cycle: LAST / Resolution: 1.98→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.07 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARMALLH3X_THBAB70ZN.PRO / Topol file: TOPALLH6X_THBAB70ZN.PRO |