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- PDB-1i73: COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i73 | ||||||
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Title | COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEASE-INHIBITOR complex / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / specific granule lumen / positive regulation of tumor necrosis factor production / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gavuzzo, E. / Pochetti, G. / Mazza, F. / Gallina, C. / Gorini, B. / D'Alessio, S. / Pieper, M. / Tschesche, H. / Tucker, P.A. | ||||||
![]() | ![]() Title: Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design. Authors: Gavuzzo, E. / Pochetti, G. / Mazza, F. / Gallina, C. / Gorini, B. / D'Alessio, S. / Pieper, M. / Tschesche, H. / Tucker, P.A. #1: ![]() Title: X-RAY STRUCTURES OF HUMAN NEUTROPHIL COLLAGENASE COMPLEXED WITH PEPTIDE HYDROXAMATE AND PEPTIDE THIOL INHIBITORS. IMPLICATIONS FOR SUBSTRATE BINDING AND RATIONAL DRUG DESIGN Authors: Grams, F. / Reinemer, P. / Powers, J.C. / Kleine, T. / Pieper, M. / Tschesche, H. / Huber, R. / Bode, W. #2: ![]() Title: Quantitative Structure-Activity Relationship of Human Neutrophil Collagenase (Mmp8-8) Inhibitors Using Comparative Molecular Field Analysis and X-Ray Structure Analysis Authors: Matter, H. / Schwab, W. / Barbier, D. / Billen, G. / Haase, B. / Neises, B. / Schudok, M. / Thorwart, W. / Schreuder, H. / Brachvogel, V. / Loenze, P. / Weithmann, K.U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.1 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.4 KB | Display | ![]() |
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Full document | ![]() | 432.8 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i76C ![]() 1japS 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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Unit cell |
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Components
#1: Protein | Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: RESIDUES 80-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 494.478 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The three residue peptide inhibitor was chemically synthesized | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES-NaOH, NaCl, CaCl2, ZnCl2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃Details: 2 micro litte of protein solution, 1 miro litter of inhibitor solution, and 5 micro litter of PEG solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 21, 1998 |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 32394 / Num. obs: 30229 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.1 / % possible all: 85.6 |
Reflection | *PLUS Num. measured all: 106034 |
Reflection shell | *PLUS % possible obs: 85.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JAP Resolution: 1.4→10 Å / Num. parameters: 14472 / Num. restraintsaints: 17466 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1203 / Occupancy sum non hydrogen: 1589 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→10 Å
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