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- PDB-1umt: Stromelysin-1 catalytic domain with hydrophobic inhibitor bound, ... -

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Basic information

Entry
Database: PDB / ID: 1umt
TitleStromelysin-1 catalytic domain with hydrophobic inhibitor bound, ph 7.0, 32oc, 20 mm cacl2, 15% acetonitrile; nmr average of 20 structures minimized with restraints
ComponentsSTROMELYSIN-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ZINC HYDROLASE / METZINCIN / MATRIX METALLOPROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / negative regulation of reactive oxygen species metabolic process / extracellular matrix disassembly ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / negative regulation of reactive oxygen species metabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / EGFR Transactivation by Gastrin / extracellular matrix / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / regulation of cell migration / cellular response to reactive oxygen species / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / protein catabolic process / metalloendopeptidase activity / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / innate immune response / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / extracellular region / zinc ion binding / nucleus / cytosol
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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-{(2S)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-L-leucyl-L-phenylalaninamide / Chem-0DS / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model type detailsminimized average
AuthorsVan Doren, S.R. / Kurochkin, A.V. / Hu, W. / Zuiderweg, E.R.P.
Citation
Journal: Protein Sci. / Year: 1995
Title: Solution structure of the catalytic domain of human stromelysin complexed with a hydrophobic inhibitor.
Authors: Van Doren, S.R. / Kurochkin, A.V. / Hu, W. / Ye, Q.Z. / Johnson, L.L. / Hupe, D.J. / Zuiderweg, E.R.
#1: Journal: Biochemistry / Year: 1993
Title: Assignments for the Main-Chain Nuclear Magnetic Resonances and Delineation of the Secondary Structure of the Catalytic Domain of Human Stromelysin-1 as Obtained from Triple-Resonance 3D NMR Experiments
Authors: Van Doren, S.R. / Kurochkin, A.V. / Ye, Q.-Z. / Johnson, L.L. / Hupe, D.J. / Zuiderweg, E.R.P.
History
DepositionOct 31, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1335
Polymers19,5141
Non-polymers6194
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: CIS PROLINE - PRO A 87
2: THR A 128 - PRO A 129 OMEGA = 137.36 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein STROMELYSIN-1 / MATRIX METALLOPROTEINASE-3 / MMP-3


Mass: 19513.646 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 83 - 256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: INDUCTION BY M13 WITH T7 RNA POLYMERASE / Gene: HUMAN STROMELYSIN-1 CATALYTIC / Plasmid: PGEMEX-D
Gene (production host): HUMAN STROMELYSIN-1 CATALYTIC DOMAIN
Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1
#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-0DS / N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-L-leucyl-L-phenylalaninamide / ICI U24522


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 448.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36N4O5
References: N-{(2S)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-L-leucyl-L-phenylalaninamide

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D HSQC
1213D CT-HNCA
1313D CT-HN(CO)CA
1413D CT-HN(CA)HA
1513D (H)CCH-TOCSY
1613D CBCA(CO)NH
171HCH
181HMQC-J
1913D NOESY-HSQC
1101HSQC-NOESY
1111HBHA(CO)NH
112113C-resolved FSCT-HSMQC-NOESY
1131half-filtered NOESY
1141filtered TOCSY
11523D CT-HA(CACO)NH
11623D CT-HA(CA)CO(N)H
11723D CT-HNCO
11832D 15N HSQC
11933D 15N-resolved NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-1.5 mM [U-99% 13C; U-99% 15N] double labeled SCD, 10 mM Tris-d11.HCl, 20 mM CaCl2, 15% acetonitrile-d3, 92% H2O/8% D2O92% H2O/8% D2O
20.6 mM [U-99% 13C; U-99% 15N] double labeled SCD, 10 mM Tris-d11.HCl, 20 mM CaCl2, 15% acetonitrile-d3, 92% H2O/8% D2O92% H2O/8% D2O
30.6 mM [U-99% 15N] N15 labeled SCD, 10 mM Tris-d11.HCl, 20 mM CaCl2, 15% acetonitrile-d3, 92% H2O/8% D2O92% H2O/8% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMdouble labeled SCD[U-99% 13C; U-99% 15N]1.0-1.51
10 mMTris-d11.HCl1
20 mMCaCl21
15 %acetonitrile-d31
0.6 mMdouble labeled SCD[U-99% 13C; U-99% 15N]2
10 mMTris-d11.HCl2
20 mMCaCl22
15 %acetonitrile-d32
0.6 mM15N labeled SCD[U-99% 15N]3
10 mMTris-d11.HCl3
20 mMCaCl23
15 %acetonitrile-d33
Sample conditionspH: 7 / Pressure: ambient / Temperature: 305 K
Crystal grow
*PLUS
Method: other

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAMX5001
Bruker AvanceBrukerAMX6002

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Processing

NMR software
NameDeveloperClassification
FelixHare Research, Inc.processing
DGIIBiosymgeometry optimization
DiscoverBiosymrefinement
RefinementSoftware ordinal: 1
Details: DISTANCE GEOMETRY (DGII INTERFACED TO INSIGHTII) FOLLOWED BY OPTIMIZATION USING SIMULATED ANNEALING WITHOUT A PHYSICAL FORCEFIELD WAS USED TO GENERATE 39 STARTING STRUCTURES. THESE 39 ...Details: DISTANCE GEOMETRY (DGII INTERFACED TO INSIGHTII) FOLLOWED BY OPTIMIZATION USING SIMULATED ANNEALING WITHOUT A PHYSICAL FORCEFIELD WAS USED TO GENERATE 39 STARTING STRUCTURES. THESE 39 STRUCTURES WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS AND RESTRAINED MINIMIZATION USING DISCOVER AND THE AMBER FORCEFIELD. THE 20 BEST STRUCTURES WITH LOWEST ENERGY AND FEWEST ABERRATIONS IN WELL-DEFINED REGIONS WERE SELECTED. RESTRAINTS INCLUDE 1336 INTERRESIDUE NOES, 55 PHI TORSION RESTRAINTS, 42 HYDROGEN BONDS, 15 METAL TO LIGAND DISTANCES, AND PEPTIDE BOND TORSION RESTRAINTS TO MAINTAIN PLANARITY. THE COMPLETE RESTRAINT LIST IS AVAILABLE AS PDB ENTRY 1UMT-MR. THE MEAN LARGEST NOE VIOLATION IS 0.64 +/- 0.07 ANGSTROM. FOR RESIDUES 83 THROUGH 250, THE MEAN BACKBONE (N, CA, C', O) RMSD TO THE AVERAGE IS 0.91 +/- 0.06 ANGSTROM. THE MEAN RMSD OF ALL HEAVY ATOMS TO THE AVERAGE IS 1.42 +/- 0.06 ANGSTROM. THIS ENSEMBLE WAS AVERAGED AND MINIMIZED WITH RESTRAINTS TO GENERATE THIS MODEL. RESIDUES 249 (167) - 256 (174) AT THE C-TERMINUS ARE DYNAMICALLY DISORDERED IN SOLUTION, JUDGING FROM THEIR LONG T2S AND LACK OF NOES. THESE RESIDUES HAVE BEEN OMITTED FROM THE MODEL.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 1 / Conformers submitted total number: 1

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