+Open data
-Basic information
Entry | Database: PDB / ID: 1gkd | ||||||
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Title | MMP9 active site mutant-inhibitor complex | ||||||
Components | 92 KDA TYPE IV COLLAGENASE | ||||||
Keywords | HYDROLASE / MATRIX METALLOPROTEASE / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information 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 / positive regulation of DNA binding ...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 / positive regulation of DNA binding / 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 / cellular response to cadmium ion / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / cellular response to reactive oxygen species / Signaling by SCF-KIT / metalloendopeptidase activity / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / endopeptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / Extra-nuclear estrogen signaling / ficolin-1-rich granule lumen / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rowsell, S. / Pauptit, R.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gkd.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gkd.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 1gkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gkd_validation.pdf.gz | 468.8 KB | Display | wwPDB validaton report |
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Full document | 1gkd_full_validation.pdf.gz | 472.8 KB | Display | |
Data in XML | 1gkd_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1gkd_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gkd ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gkd | HTTPS FTP |
-Related structure data
Related structure data | 1gkcSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.21819, -0.95291, -0.21059), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18383.424 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN RESIDUES 107-215,391-443 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14780, gelatinase B |
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-Non-polymers , 5 types, 200 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE INITIAL METHIONINE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: PROTEIN SOLUTION (4MG/ML IN 20MM TRIS-HCL PH 7.5, 50MM NACL) WAS INCUBATED WITH 5MM INHIBITOR FOR 30MINS PRIOR TO SETTING UP CRYSTALLISATION TRIALS. THE CRYSTALLISATION DROPS CONTAINED A 1:1 ...Details: PROTEIN SOLUTION (4MG/ML IN 20MM TRIS-HCL PH 7.5, 50MM NACL) WAS INCUBATED WITH 5MM INHIBITOR FOR 30MINS PRIOR TO SETTING UP CRYSTALLISATION TRIALS. THE CRYSTALLISATION DROPS CONTAINED A 1:1 MIXTURE OF COMPLEX SOLUTION AND RESERVOIR BUFFER (2.6 - 2.8 M NACL, 0.1 M HEPES PH 9.0). | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.5 / 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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 22, 2000 / 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: 2.1→36.3 Å / Num. obs: 18276 / % possible obs: 70 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.1→2.27 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.385 / % possible all: 40 |
Reflection | *PLUS Highest resolution: 2.1 Å / % possible obs: 71.2 % / Num. measured all: 50609 |
Reflection shell | *PLUS % possible obs: 40.4 % / Num. unique obs: 2038 / Num. measured obs: 3391 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WILD-TYPE MMP-9 STRUCTURE (1GKC) Resolution: 2.1→36.3 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: MASK / Bsol: 58.27 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→36.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 1.08 Å2 / Rms dev position: 0.1 Å / Weight Biso : 2 / Weight position: 50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 36.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.266 |