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Yorodumi- PDB-1d2b: THE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d2b | ||||||
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Title | THE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR OF METALLOPROTEINASES-1 (N-TIMP-1), SOLUTION NMR, 29 STRUCTURES | ||||||
Components | Metalloproteinase inhibitor 1Matrix metalloproteinase inhibitor | ||||||
Keywords | HYDROLASE INHIBITOR / OB-FOLD / BETA BARREL / PROTEASE INHIBITOR / MMP INHIBITOR | ||||||
Function / homology | Function and homology information regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / peptidase inhibitor activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity / negative regulation of endopeptidase activity ...regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / peptidase inhibitor activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity / negative regulation of endopeptidase activity / cartilage development / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / basement membrane / response to hormone / extracellular matrix / platelet alpha granule lumen / response to cytokine / cytokine activity / Post-translational protein phosphorylation / growth factor 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 / Interleukin-4 and Interleukin-13 signaling / protease binding / endoplasmic reticulum lumen / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS, CARTESIAN SIMULATED ANNEALING | ||||||
Authors | Wu, B. / Arumugam, S. / Semenchenko, V. / Brew, K. / Van Doren, S.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: NMR structure of tissue inhibitor of metalloproteinases-1 implicates localized induced fit in recognition of matrix metalloproteinases. Authors: Wu, B. / Arumugam, S. / Gao, G. / Lee, G.I. / Semenchenko, V. / Huang, W. / Brew, K. / Van Doren, S.R. #1: Journal: J.Biomol.NMR / Year: 1999 Title: 1H, 13C and 15N Resonance Assignments and Secondary Structure of the N- Terminal Domain of Human Tissue Inhibitor of Metalloproteinases-1 Authors: Wu, B. / Arumugam, S. / Huang, W. / Brew, K. / Van Doren, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d2b.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1d2b.ent.gz | 955.8 KB | Display | PDB format |
PDBx/mmJSON format | 1d2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/1d2b ftp://data.pdbj.org/pub/pdb/validation_reports/d2/1d2b | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14269.307 Da / Num. of mol.: 1 / Fragment: NTR domain, residues 24-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: THIS IS THE FIRST 126 RESIDUES OF THE FULL LENGTH OF 184 RESIDUES NATURALLY OCCURRING IN HUMANS. THE 126 RESIDUE RECOMBINANT N-TERMINAL DOMAIN LACKS THE NATURAL N-LINKED GLYCOSYLATION OF ASN30 AND ASN78. Cellular location: EXTRACELLULAR MATRIX / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P01033 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: 3D HNHB, 3D HACAHB-COSY, 2D HMQC-J, 3D COUPLED HCACO, 3D HNCA-J, {15N} SPIN- ECHO DIFFERENCE 13C CT-HSQC, {13CO} SPIN-ECHO DIFFERENCE 13C CT-HSQC, 2D HN(CG) , 2D HN(COCG), 15N IPAP-HSQC, 3D ...Text: 3D HNHB, 3D HACAHB-COSY, 2D HMQC-J, 3D COUPLED HCACO, 3D HNCA-J, {15N} SPIN- ECHO DIFFERENCE 13C CT-HSQC, {13CO} SPIN-ECHO DIFFERENCE 13C CT-HSQC, 2D HN(CG) , 2D HN(COCG), 15N IPAP-HSQC, 3D 13CA-COUPLED HNCO, 13C'-COUPLED IN-PHASE 15N HSQC |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 0.171 / pH: 6.0 / Pressure: AMBIENT / Temperature: 293 K | ||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS, CARTESIAN SIMULATED ANNEALING Software ordinal: 3 Details: Model 22 is closest to the average while Model 3 represents the conformer with the fewest violations | ||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 120 / Conformers submitted total number: 29 |