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- PDB-1dlk: CRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dlk | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTIDYL CHLOROMETHYL KETONE INHIBITOR | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Delta-chymotrypsin / peptidic inhibior / chloromethyl ketone / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 | ![]() ![]() | ||||||
![]() | Mac Sweeney, A. / Birrane, G. / Walsh, M.A. / O'Connell, T. / Malthouse, J.P.G. | ||||||
![]() | ![]() Title: Crystal structure of delta-chymotrypsin bound to a peptidyl chloromethyl ketone inhibitor. Authors: Mac Sweeney, A. / Birrane, G. / Walsh, M.A. / O'Connell, T. / Malthouse, J.P. / Higgins, T.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 | ![]() | 106.9 KB | Display | ![]() |
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PDB format | ![]() | 87.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.6 KB | Display | ![]() |
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Full document | ![]() | 485.5 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.03684, -0.49183, 0.86991), Vector: |
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Components
#1: Protein/peptide | Mass: 1253.511 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-13 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 24206.271 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-245 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein/peptide | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Compound details | THE PEPTIDIC INHIBITOR BINDS TO THROMBIN THROUGH TWO COVALENT BONDS: A BOND BETWEEN 0QE AND HIS 57 ...THE PEPTIDIC INHIBITOR BINDS TO THROMBIN THROUGH TWO COVALENT BONDS: A BOND BETWEEN 0QE AND HIS 57 AND A HEMIKETAL BETWEEN HPH AND SER 195. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.59 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.6 M ammonium sulfate, 200 mM MES-HCl, 10 mM CoCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.911 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→40 Å / Num. all: 48065 / Num. obs: 39978 / % possible obs: 82.7 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.14→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.43 / Num. unique all: 2370 / % possible all: 100 |
Reflection | *PLUS Num. obs: 48065 / % possible obs: 99.6 % / Num. measured all: 308959 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.3 |
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Processing
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Refinement | Resolution: 2.14→19.9 Å / σ(F): 0 / Stereochemistry target values: John Priestle / Details: Used maximum likelihood procedure
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Refinement step | Cycle: LAST / Resolution: 2.14→19.9 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / Num. reflection obs: 48013 / σ(F): 0 / Num. reflection Rfree: 2370 / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.251 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 2 |