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Open data
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Basic information
Entry | Database: PDB / ID: 1gkc | ||||||
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Title | MMP9-inhibitor complex | ||||||
![]() | 92 KDA TYPE IV COLLAGENASE | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / MATRIX METALLOPROTEASE / HYDROLASE / GLYCOPROTEIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rowsell, S. / Pauptit, R.A. | ||||||
![]() | ![]() Title: Crystal Structure of Mmp9 in Complex with a Reverse Hydroxamate Inhibitor Authors: Rowsell, S. / Hawtin, P. / Minshull, C.A. / Jepson, H. / Brockbank, S. / Barratt, D. / Slater, A.M. / Mcpheat, W. / Waterson, D. / Henney, A. / Pauptit, R.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 | ![]() | 83.7 KB | Display | ![]() |
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PDB format | ![]() | 62.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 981.3 KB | Display | ![]() |
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Full document | ![]() | 986.4 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gkdC ![]() 1hfsS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.22861, -0.9625, 0.14604), Vector: |
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Components
#1: Protein | Mass: 18384.408 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN RESIDUES 107-215,391-443 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Sequence details | THE INITIAL METHIONINE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: THE CRYSTALLISATION DROPS CONTAINED A 1:1 MIXTURE OF PURIFIED COMPLEX SOLUTION (0.55 MG/ML PROTEIN AND 0.5 MM INHIBITOR SOLUTION CONCENTRATED TO ~4 MG/ML IN 20 MM TRIS- HCL PH 7.5, 2 MM ...Details: THE CRYSTALLISATION DROPS CONTAINED A 1:1 MIXTURE OF PURIFIED COMPLEX SOLUTION (0.55 MG/ML PROTEIN AND 0.5 MM INHIBITOR SOLUTION CONCENTRATED TO ~4 MG/ML IN 20 MM TRIS- HCL PH 7.5, 2 MM CACL2, 50 MM NACL) AND RESERVOIR BUFFER (3.6 M NACL, 0.1 M HEPES PH 7.5). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 25, 1999 / Details: SILICON MIRROR |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→51.3 Å / Num. obs: 17375 / % possible obs: 88 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.479 / % possible all: 83 |
Reflection | *PLUS Highest resolution: 2.3 Å / % possible obs: 88.3 % / Num. measured all: 77726 |
Reflection shell | *PLUS % possible obs: 83.3 % / Num. unique obs: 2656 / Num. measured obs: 10147 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HFS Resolution: 2.3→51.3 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: X-PLOR, CNS
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Solvent computation | Solvent model: MASK / Bsol: 47.85 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→51.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 2.6 Å2 / Rms dev position: 0.09 Å / Weight Biso : 2 / Weight position: 50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 51.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.277 |