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- PDB-1eub: SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3... -

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Entry
Database: PDB / ID: 1eub
TitleSOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR
ComponentsCOLLAGENASE 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ALPHA HELIX / BETA SHEET / PROTEIN-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


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
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
3-METHYLPYRIDINE / HYDROXYAMINOVALINE / 1-METHYLOXY-4-SULFONE-BENZENE / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, ENERGY MINIMIZATION
AuthorsZhang, X. / Gonnella, N.C. / Koehn, J. / Pathak, N. / Ganu, V. / Melton, R. / Parker, D. / Hu, S.I. / Nam, K.Y.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Solution structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent non-peptidic sulfonamide inhibitor: binding comparison with stromelysin-1 and collagenase-1.
Authors: Zhang, X. / Gonnella, N.C. / Koehn, J. / Pathak, N. / Ganu, V. / Melton, R. / Parker, D. / Hu, S.I. / Nam, K.Y.
History
DepositionApr 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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_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_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.pdbx_leaving_atom_flag / _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)19,8448
Polymers19,2351
Non-polymers6087
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,TARGET FUNCTION
RepresentativeModel #1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein COLLAGENASE 3 / MATRIX METALLOPROTEINASE-13 / MMP-13


Mass: 19235.383 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3D-CD-CLN3 / Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 7 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HAV / HYDROXYAMINOVALINE


Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#5: Chemical ChemComp-3MP / 3-METHYLPYRIDINE


Mass: 93.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N
#6: Chemical ChemComp-MSB / 1-METHYLOXY-4-SULFONE-BENZENE


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D 15N EDITED NOESY
1312D 15N HSQC
1412D 13C HMQC
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D HN(CA)CB
1813D HNCO
1912D 13C
110115N FILTERED NOESY
11112D 13C FILTERED NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING 2D AND 3D HETERONUCLEAR NMR TECHNIQUES

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Sample preparation

DetailsContents: 0.5 MM COLLAGENASE-3 15N, 13C, 20 MM TRIS D11, 20 MM CACL2, 0.02% NAN3, 5 MM DTT, 100 MM NACL, 0.1 MM ZNCL,
Sample conditionsIonic strength: 100 mM NACL / pH: 6.80 / Pressure: AMBIENT / Temperature: 310.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR98.1BRUNGERrefinement
Felix97structure solution
NMRCompass2.5structure solution
Insight II98structure solution
QUANTA97structure solution
RefinementMethod: SIMULATED ANNEALING, ENERGY MINIMIZATION / Software ordinal: 1
NMR ensembleConformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,TARGET FUNCTION
Conformers calculated total number: 50 / Conformers submitted total number: 20

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