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- PDB-2j0t: Crystal Structure of the Catalytic Domain of MMP-1 in Complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j0t | ||||||
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Title | Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1 | ||||||
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![]() | HYDROLASE / EXTRACELLULAR MATRIX / ERYTHROCYTE MATURATION / AUTOCATALYTIC CLEAVAGE / COLLAGEN DEGRADATION | ||||||
Function / homology | ![]() regulation of integrin-mediated signaling pathway / interstitial collagenase / negative regulation of metallopeptidase activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity ...regulation of integrin-mediated signaling pathway / interstitial collagenase / negative regulation of metallopeptidase activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity / negative regulation of endopeptidase activity / protein metabolic process / cartilage development / Basigin interactions / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / Collagen degradation / basement membrane / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / platelet alpha granule lumen / response to hormone / response to cytokine / cytokine activity / Post-translational protein phosphorylation / growth factor activity / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / response to peptide hormone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / protease binding / endoplasmic reticulum lumen / serine-type endopeptidase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Iyer, S. / Wei, S. / Brew, K. / Acharya, K.R. | ||||||
![]() | ![]() Title: Crystal Structure of the Catalytic Domain of Matrix Metalloproteinase-1 in Complex with the Inhibitory Domain of Tissue Inhibitor of Metalloproteinase-1. Authors: Iyer, S. / Wei, S. / Brew, K. / Acharya, K.R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
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PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.3 KB | Display | ![]() |
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Full document | ![]() | 509.1 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Components
#1: Protein | Mass: 18996.736 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 101-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 14269.307 Da / Num. of mol.: 3 / Fragment: N-TERMINAL INHIBITORY DOMAIN, RESIDUES 24-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Compound details | CLEAVES COLLAGENS OF TYPES I, II, AND III AT ONE SITE IN THE HELICAL DOMAIN. ALSO CLEAVES COLLAGENS ...CLEAVES COLLAGENS OF TYPES I, II, AND III AT ONE SITE IN THE HELICAL DOMAIN. ALSO CLEAVES COLLAGENS OF TYPES VII AND X. COMPLEXES WITH METALLOPRO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | pH: 7.5 Details: 10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 23, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→40 Å / Num. obs: 29526 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.54→2.63 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1CGL AND 1UEA Resolution: 2.54→23 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.892 / SU B: 29.759 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.118 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED AS ALANINES OR GLYCINES.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→23 Å
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Refine LS restraints |
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