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- PDB-1fm1: SOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT OF HUMAN COLLAGENASE... -
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Basic information
Entry | Database: PDB / ID: 1fm1 | ||||||
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Title | SOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED WITH A HYDROXAMIC ACID INHIBITOR | ||||||
![]() | COLLAGENASE-3 | ||||||
![]() | HYDROLASE / Matrix Metalloproteinase / Hydroxamic acid / Human Collagenase-3 / MMP-13 | ||||||
Function / homology | ![]() growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing | ||||||
![]() | Moy, F.J. / Chanda, P.K. / Chen, J.M. / Cosmi, S. / Edris, W. / Levin, J.I. / Powers, R. | ||||||
![]() | ![]() Title: High-resolution solution structure of the catalytic fragment of human collagenase-3 (MMP-13) complexed with a hydroxamic acid inhibitor. Authors: Moy, F.J. / Chanda, P.K. / Chen, J.M. / Cosmi, S. / Edris, W. / Levin, J.I. / Powers, R. #1: ![]() Title: 1H, 15N, 13C, and 13CO Assignments and Secondary Structure Determination of Collagenase-3 (MMP-13) Complexed with a Hydroxamic Acid Inhibitor Authors: Moy, F.J. / Chanda, P.K. / Cosmi, S. / Edris, W. / Levin, J.I. / Powers, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 662.8 KB | Display | |
Data in XML | ![]() | 118 KB | Display | |
Data in CIF | ![]() | 136 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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NMR ensembles |
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Components
#1: Protein | Mass: 18607.824 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT Source method: isolated from a genetically manipulated source Details: HYDROXAMIC ACID INHIBITOR COMPLEX / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-WAY / | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance and isotope filtered NMR spectroscopy. |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT pH: 6.5 / Pressure: ambient / Temperature: 308 K | ||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX 2 / Manufacturer: Bruker / Model: AMX 2 / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: distance geometry simulated annealing / Software ordinal: 1 Details: structures calculated were based on 3280 experimental NMR restraints, consisting of 2415 approximate interproton distance restraints, 47 distance restraints between MMP-13 and WAY-151693, 5 ...Details: structures calculated were based on 3280 experimental NMR restraints, consisting of 2415 approximate interproton distance restraints, 47 distance restraints between MMP-13 and WAY-151693, 5 intramolecular distance restraints for WAY-151693, 88 distance restraints for 44 backbone hydrogen bonds, 391 torsion angle restraints, 103 3JNHa restraints 123 Ca restraints and 108 Cb restraints. The structure was also refined using a conformational database. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function Conformers calculated total number: 100 / Conformers submitted total number: 30 |