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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
TitleSOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED WITH A HYDROXAMIC ACID INHIBITOR
ComponentsCOLLAGENASE-3
KeywordsHYDROLASE / Matrix Metalloproteinase / Hydroxamic acid / Human Collagenase-3 / MMP-13
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / bone morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / 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 / bone morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / 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
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-WAY / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsMoy, F.J. / Chanda, P.K. / Chen, J.M. / Cosmi, S. / Edris, W. / Levin, J.I. / Powers, R.
Citation
Journal: J.Mol.Biol. / Year: 2000
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: Journal: J.Biomol.NMR / Year: 2000
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.
History
DepositionAug 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLLAGENASE-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2065
Polymers18,6081
Non-polymers5984
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Representative

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Components

#1: Protein COLLAGENASE-3 / MMP-13


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.) Homo sapiens (human) / Plasmid: PPROMMP-13 / Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-WAY / N-HYDROXY-2-[(4-METHOXY-BENZENESULFONYL)-PYRIDIN-3-YLMETHYL-AMINO]-3-METHYL-BENZAMIDE / WAY-151693


Mass: 427.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O5S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1233D 15N-separated NOESY
132HNHA
1413D C13-edited/filtered-NOESY
NMR detailsText: The structure was determined using triple-resonance and isotope filtered NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM of U-15N,13C MMP-13 in an equimolar complex with WAY-151693 in a buffer containing 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT, in 100% D2O at pH 6.5 and 35C100% D2O
21 mM of U-15N,13C MMP-13 in an equimolar complex with WAY-151693 in a buffer containing 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT, in 90% H2O, 10% D2O at pH 6.5 and 35C90% H2O/10% D2O
31 mM of U-15N MMP-13 in an equimolar complex with WAY-151693 in a buffer containing 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT, in 90% H2O, 10% D2O at pH 6.5 and 35C90% H2O/10% D2O
Sample conditionsIonic 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

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NMR measurement

NMR spectrometerType: Bruker AMX 2 / Manufacturer: Bruker / Model: AMX 2 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
NMRPipe1.7Delaglioprocessing
X-PLOR3.84Brungerstructure solution
PIPP4.2.8Garrettdata analysis
X-PLOR3.84Brungerrefinement
RefinementMethod: 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 ensembleConformer 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

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