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- PDB-3vgc: GAMMA-CHYMOTRYPSIN L-NAPHTHYL-1-ACETAMIDO BORONIC ACID ACID INHIB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vgc | ||||||
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Title | GAMMA-CHYMOTRYPSIN L-NAPHTHYL-1-ACETAMIDO BORONIC ACID ACID INHIBITOR COMPLEX | ||||||
![]() | (GAMMA CHYMOTRYPSIN) x 3 | ||||||
![]() | SERINE PROTEASE / HYDROLASE | ||||||
Function / homology | ![]() chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Stoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F. | ||||||
![]() | ![]() Title: Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Authors: Stoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F. #1: ![]() Title: Probing the Specificity of the Serine Proteases Subtilisin Carlsberg and A-Chymotrypsin with Enantiomeric 1-Acetamido Boronic Acids. An Unexpected Reversal of the Normal Authors: Martichonok, V. / Jones, J.B. #2: ![]() Title: Probing the Specificity of the S1 Binding Site of Subtilisin Carlsberg with Boronic Acids Authors: Seufer-Wasserthal, P. / Martichonok, V. / Keller, T.H. / Chin, B. / Martin, R. / Jones, J.B. #3: ![]() Title: Gamma-Chymotrypsin is a Complex of Alpha-Chymotrypsin with its Own Autolysis Products Authors: Harel, M. / Su, C.T. / Frolow, F. / Silman, I. / Sussman, J.L. #4: ![]() Title: Structure and Activity of Two Photoreversible Cinnamates Bound to Chymotrypsin Authors: Stoddard, B.L. / Bruhnke, J. / Porter, N. / Ringe, D. / Petsko, G.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 | ![]() | 56.1 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.8 KB | Display | ![]() |
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Full document | ![]() | 818.9 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1av7C ![]() 1avtC ![]() 1vgcC ![]() 1vsbC ![]() 2vgcC ![]() 3vsbC ![]() 4vgcC ![]() 3gchS S: Starting model for refinement 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: A-CHYMOTRYPSIN PURCHASED FROM SIGMA AND CONVERTED TO G-CHYMOTRYPSIN BY THE METHOD OF STODDARD ET AL., 1990, BIOCHEMISTRY, VOL. 29, P. 4871-4879 Source: (natural) ![]() ![]() |
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-Protein , 2 types, 2 molecules BC
#2: Protein | Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: A-CHYMOTRYPSIN PURCHASED FROM SIGMA AND CONVERTED TO G-CHYMOTRYPSIN BY THE METHOD OF STODDARD ET AL., 1990, BIOCHEMISTRY, VOL. 29, P. 4871-4879 Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: A-CHYMOTRYPSIN PURCHASED FROM SIGMA AND CONVERTED TO G-CHYMOTRYPSIN BY THE METHOD OF STODDARD ET AL., 1990, BIOCHEMISTRY, VOL. 29, P. 4871-4879 Source: (natural) ![]() ![]() |
-Non-polymers , 3 types, 100 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/SRB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SRB.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-SRB / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED IN SCINTILLATION VIALS IN 65% AMMONIUM SULFATE, 100 MM CACODYLATE, PH 6.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Stoddard, B.L., (1990) Biochemistry, 29, 4871. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1995 / Details: FRANKS MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→10 Å / Num. obs: 25288 / % possible obs: 84.7 % / Observed criterion σ(I): 1 / Redundancy: 5.18 % / Rsym value: 0.066 |
Reflection shell | Resolution: 1.67→1.75 Å / Rsym value: 0.273 / % possible all: 36.59 |
Reflection | *PLUS Rmerge(I) obs: 0.066 |
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Processing
Software |
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Refinement | Method to determine structure: DIRECT SOLUTION WITH KNOWN STRUCTURE Starting model: PDB ENTRY 3GCH Resolution: 1.67→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
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Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.75 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2425 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.32749 |