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- PDB-1g4k: X-ray Structure of a Novel Matrix Metalloproteinase Inhibitor Com... -

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Basic information

Entry
Database: PDB / ID: 1g4k
TitleX-ray Structure of a Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
ComponentsSTROMELYSIN-1Matrix metalloproteinase
KeywordsHYDROLASE / stomelysin / MMP / zinc ligand
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 / 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 / negative regulation of reactive oxygen species metabolic process / cellular response to nitric oxide / extracellular matrix disassembly / 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 / positive regulation of protein-containing complex assembly / protein catabolic process / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / 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-HQQ / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDunten, P. / Kammlott, U. / Crowther, R. / Levin, W. / Foley, L.H. / Wang, P. / Palermo, R.
CitationJournal: Protein Sci. / Year: 2001
Title: X-ray structure of a novel matrix metalloproteinase inhibitor complexed to stromelysin.
Authors: Dunten, P. / Kammlott, U. / Crowther, R. / Levin, W. / Foley, L.H. / Wang, P. / Palermo, R.
History
DepositionOct 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Feb 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_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_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
C: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,43722
Polymers56,6613
Non-polymers1,77619
Water3,369187
1
A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4487
Polymers18,8871
Non-polymers5616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5408
Polymers18,8871
Non-polymers6537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4487
Polymers18,8871
Non-polymers5616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.800, 103.800, 147.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein STROMELYSIN-1 / Matrix metalloproteinase


Mass: 18887.029 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1

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Non-polymers , 5 types, 206 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HQQ / 5-METHYL-5-(4-PHENOXY-PHENYL)-PYRIMIDINE-2,4,6-TRIONE


Mass: 310.304 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H14N2O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-MME 5000, ammonium sulfate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: drop consists of 2 micro litter of protein solution and 1 micro litter of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
35 mM1dropCaCl2
40.02 %1dropNaN3
52.5 mMinhibitor1drop
60.2 Mammonium sulfate1reservoir
730 %mPEG50001reservoir
80.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 12, 1998
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 55161 / Num. obs: 55161 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.121 / Num. unique all: 5414 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 5554 -random
Rwork0.244 ---
obs-54951 99.9 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 90 187 4294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.032

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