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- PDB-1hov: SOLUTION STRUCTURE OF A CATALYTIC DOMAIN OF MMP-2 COMPLEXED WITH ... -

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Entry
Database: PDB / ID: 1hov
TitleSOLUTION STRUCTURE OF A CATALYTIC DOMAIN OF MMP-2 COMPLEXED WITH SC-74020
ComponentsMATRIX METALLOPROTEINASE-2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / enzyme-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle ...gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / prostate gland epithelium morphogenesis / protein metabolic process / cellular response to fluid shear stress / negative regulation of cell adhesion / face morphogenesis / negative regulation of vasoconstriction / Activation of Matrix Metalloproteinases / endodermal cell differentiation / macrophage chemotaxis / response to amyloid-beta / fibronectin binding / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / response to hyperoxia / cellular response to interleukin-1 / response to electrical stimulus / response to mechanical stimulus / response to retinoic acid / ovarian follicle development / positive regulation of vascular associated smooth muscle cell proliferation / embryo implantation / Degradation of the extracellular matrix / sarcomere / extracellular matrix organization / response to activity / cellular response to estradiol stimulus / cellular response to amino acid stimulus / response to nicotine / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / cellular response to reactive oxygen species / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / heart development / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / Extra-nuclear estrogen signaling / response to hypoxia / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / plasma membrane
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / 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 / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-I52 / 72 kDa type IV collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsFeng, Y. / Likos, J.J. / Zhu, L. / Woodward, H. / Munie, G. / McDonald, J.J. / Stevens, A.M. / Howard, C.P. / De Crescenzo, G.A. / Welsch, D. ...Feng, Y. / Likos, J.J. / Zhu, L. / Woodward, H. / Munie, G. / McDonald, J.J. / Stevens, A.M. / Howard, C.P. / De Crescenzo, G.A. / Welsch, D. / Shieh, H.-S. / Stallings, W.C.
Citation
Journal: Biochim.Biophys.Acta / Year: 2002
Title: Solution structure and backbone dynamics of the catalytic domain of matrix metalloproteinase-2 complexed with a hydroxamic acid inhibitor
Authors: Feng, Y. / Likos, J.J. / Zhu, L. / Woodward, H. / Munie, G. / McDonald, J.J. / Stevens, A.M. / Howard, C.P. / De Crescenzo, G.A. / Welsch, D. / Shieh, H.-S. / Stallings, W.C.
#1: Journal: J.Biomol.NMR / Year: 2000
Title: 1H, 13C and 15N resonance assignments for a truncated and inhibited catalytic domain of matrix metalloproteinase-2
History
DepositionDec 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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.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:
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Assembly

Deposited unit
A: MATRIX METALLOPROTEINASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2776
Polymers18,4911
Non-polymers7865
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 14structures with the least restraint violations
RepresentativeModel #3reasonable inhibitor conformation

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Components

#1: Protein MATRIX METALLOPROTEINASE-2


Mass: 18491.391 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): W3110-II5 / References: UniProt: P08253, gelatinase A
#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-I52 / N-{4-[(1-HYDROXYCARBAMOYL-2-METHYL-PROPYL)-(2-MORPHOLIN-4-YL-ETHYL)-SULFAMOYL]-4-PENTYL-BENZAMIDE / SC-74020


Mass: 574.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H42N4O6S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 0.3-0.4mM U-15N, 13C MMP-2C: unlabeled SC-74020 in 20mM TRIS-d11-HCl, 5mM CaCl2, 10uM ZnCl2, 20uM unlabeled SC-74020
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR98.1MSIrefinement
VNMR6.1bVariancollection
Felix97MSIdata analysis
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: reasonable inhibitor conformation
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 14 / Conformers submitted total number: 11

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