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- PDB-1hy7: A CARBOXYLIC ACID BASED INHIBITOR IN COMPLEX WITH MMP3 -

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Basic information

Entry
Database: PDB / ID: 1hy7
TitleA CARBOXYLIC ACID BASED INHIBITOR IN COMPLEX WITH MMP3
ComponentsSTROMELYSIN-1
KeywordsHYDROLASE / mixed alpha beta structure / zinc protease / inhibited
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 / extracellular matrix disassembly / cellular response to nitric oxide ...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 / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to amino acid stimulus / protein catabolic process / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol
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-MBS / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsNatchus, M.G. / Bookland, R.G. / Laufersweiler, M.J. / Pikul, S. / Almstead, N.G. / De, B. / Janusz, M.J. / Hsieh, L.C. / Gu, F. / Pokross, M.E. ...Natchus, M.G. / Bookland, R.G. / Laufersweiler, M.J. / Pikul, S. / Almstead, N.G. / De, B. / Janusz, M.J. / Hsieh, L.C. / Gu, F. / Pokross, M.E. / Patel, V.S. / Garver, S.M. / Peng, S.X. / Branch, T.M. / King, S.L. / Baker, T.R. / Foltz, D.J. / Mieling, G.E.
CitationJournal: J.Med.Chem. / Year: 2001
Title: Development of new carboxylic acid-based MMP inhibitors derived from functionalized propargylglycines.
Authors: Natchus, M.G. / Bookland, R.G. / Laufersweiler, M.J. / Pikul, S. / Almstead, N.G. / De, B. / Janusz, M.J. / Hsieh, L.C. / Gu, F. / Pokross, M.E. / Patel, V.S. / Garver, S.M. / Peng, S.X. / ...Authors: Natchus, M.G. / Bookland, R.G. / Laufersweiler, M.J. / Pikul, S. / Almstead, N.G. / De, B. / Janusz, M.J. / Hsieh, L.C. / Gu, F. / Pokross, M.E. / Patel, V.S. / Garver, S.M. / Peng, S.X. / Branch, T.M. / King, S.L. / Baker, T.R. / Foltz, D.J. / Mieling, G.E.
History
DepositionJan 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _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
B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73913
Polymers38,8332
Non-polymers90611
Water6,053336
1
A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6686
Polymers19,4171
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0717
Polymers19,4171
Non-polymers6556
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: STROMELYSIN-1
hetero molecules

B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73913
Polymers38,8332
Non-polymers90611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_464-x-1/2,-y+1,z-1/21
Buried area2500 Å2
ΔGint-135 kcal/mol
Surface area16720 Å2
MethodPISA, PQS
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.918, 78.059, 105.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer constructed from chain A or chain B

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Components

#1: Protein STROMELYSIN-1 / MMP-3


Mass: 19416.529 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 100-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: FIBROBLAST / Gene: MMP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MBS / R-2-{[4'-METHOXY-(1,1'-BIPHENYL)-4-YL]-SULFONYL}-AMINO-6-METHOXY-HEX-4-YNOIC ACID


Mass: 403.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21NO6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, sodium chloride, magnesium chloride, Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 30, 2000 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→17.398 Å / Num. all: 49934 / Num. obs: 47986 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 15.532 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / Num. unique all: 3963 / % possible all: 78.4

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Processing

Software
NameClassification
FFTmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→63.25 Å / Isotropic thermal model: isotropic / Cross valid method: Free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelyhood procedures
RfactorNum. reflection% reflectionSelection details
Rfree0.22039 2529 -random
Rwork0.18829 ---
obs0.18992 46098 97.4 %-
all-47329 --
Displacement parametersBiso mean: 18.967 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å21 Å2-0.5 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 38 336 3021
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_deg1.725
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_mcbond_it1.038
X-RAY DIFFRACTIONp_mcangle_it1.796
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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