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- PDB-2k2g: Solution structure of the wild-type catalytic domain of human mat... -

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Basic information

Entry
Database: PDB / ID: 2k2g
TitleSolution structure of the wild-type catalytic domain of human matrix metalloproteinase 12 (MMP-12) in complex with a tight-binding inhibitor
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / macrophage elastase / matrix metalloproteinase / protein-ligand structure / catalytic domain / human gene / Calcium / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / cellular response to virus / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
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
N-(dibenzo[b,d]thiophen-3-ylsulfonyl)-L-valine / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing
Model detailsensemble of 17 structures
AuthorsMarkus, M.A. / Dwyer, B. / Wolfrom, S. / Li, J. / Li, W. / Malakian, K. / Wilhelm, J. / Tsao, D.H.H.
Citation
Journal: J.Biomol.Nmr / Year: 2008
Title: Solution structure of wild-type human matrix metalloproteinase 12 (MMP-12) in complex with a tight-binding inhibitor.
Authors: Markus, M.A. / Dwyer, B. / Wolfrom, S. / Li, J. / Li, W. / Malakian, K. / Wilhelm, J. / Tsao, D.H.
#1: Journal: J.Biomol.NMR / Year: 2005
Title: 1H, 13C, and 15N assignments of MMP-12, a key protease implicated in lung tissue remodeling
Authors: Markus, M.A. / Dwyer, B. / Wolfrom, S. / Li, J. / Li, W. / Malakian, K. / Wilhelm, J. / Tsao, D.H.H.
History
DepositionApr 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 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: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8614
Polymers18,3671
Non-polymers4943
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Macrophage metalloelastase / HME / Matrix metalloproteinase-12 / MMP-12 / Macrophage elastase / ME


Mass: 18366.605 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 100 to 263)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39900, macrophage elastase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DSV / N-(dibenzo[b,d]thiophen-3-ylsulfonyl)-L-valine


Mass: 363.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17NO4S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: ensemble of 17 structures
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNHA
1353D HNHB
1423D HACACB
1523D LRCC
1613D 1H-15N NOESY
1713D 13C-15N NOESY
1813D 1H-15N NOESY
1923D 1H-13C NOESY
11023D 13C-12C NOESY
11142D 1H-15N HSQC IPAP
11262D 1H-15N HSQC no C' decoupling
11363D HNCO no Ca decoupling
11463D HACA(CO)NH no Ha decoupling
NMR detailsText: Chemical shift assignments were previously reported, so experiments to support the assignments will not be described.

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Sample preparation

Details
Solution-IDContentsSolvent system
1700 uM [U-100% 13C; U-100% 15N] protein, 700 uM DSV, 93% H2O/7% D2O93% H2O/7% D2O
2400 uM [U-100% 13C; U-100% 15N] protein, 400 uM DSV, 100% D2O100% D2O
3550 uM [U-10% 13C] protein, 550 uM DSV, 100% D2O100% D2O
4400 uM [U-100% 15N] protein, 400 uM DSV, 93% H2O/7% D2O93% H2O/7% D2O
5400 uM [U-100% 15N] protein, 400 uM DSV, 93% H2O/7% D2O93% H2O/7% D2O
6250 uM [U-100% 13C; U-100% 15N] protein, 250 uM DSV, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
700 uMprotein[U-100% 13C; U-100% 15N]1
700 uMDSV1
400 uMprotein[U-100% 13C; U-100% 15N]2
400 uMDSV2
550 uMprotein[U-10% 13C]3
550 uMDSV3
400 uMprotein[U-100% 15N]4
400 uMDSV4
400 uMprotein[U-100% 15N]5
400 uMDSV5
250 uMprotein[U-100% 13C; U-100% 15N]6
250 uMDSV6
Sample conditionsIonic strength: 160 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1
Details: for structures with NOE and angle restraints, to incorporate dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 17

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