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- PDB-2srt: CATALYTIC DOMAIN OF HUMAN STROMELYSIN-1 AT PH 5.5 AND 40OC COMPLE... -

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Entry
Database: PDB / ID: 2srt
TitleCATALYTIC DOMAIN OF HUMAN STROMELYSIN-1 AT PH 5.5 AND 40OC COMPLEXED WITH INHIBITOR
ComponentsSTROMELYSIN-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METZINCIN / 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
Chem-8MI / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsGooley, P.R. / O'Connell, J.F.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: The NMR structure of the inhibited catalytic domain of human stromelysin-1.
Authors: Gooley, P.R. / O'Connell, J.F. / Marcy, A.I. / Cuca, G.C. / Salowe, S.P. / Bush, B.L. / Hermes, J.D. / Esser, C.K. / Hagmann, W.K. / Springer, J.P. / Johnson, B.A.
#1: Journal: Biochemistry / Year: 1993
Title: Secondary Structure and Zinc Ligation of Human Recombinant Short-Form Stromelysin by Multidimensional Heteronuclear NMR
Authors: Gooley, P.R. / Johnson, B.A. / Marcy, A.I. / Cuca, G.C. / Salowe, S.P. / Hagmann, W.K. / Esser, C.K. / Springer, J.P.
History
DepositionMar 22, 1995Processing site: BNL
SupersessionJul 10, 1995ID: 1SRT
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 2.0Sep 29, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1May 22, 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: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0314
Polymers19,4171
Non-polymers6143
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: GLU 150 - HIS 151 MODEL 24 OMEGA = 139.66 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / -
Representative

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Components

#1: Protein STROMELYSIN-1


Mass: 19416.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN STROMELYSIN-1 / Plasmid: PRO-SFSTR / Gene (production host): HUMAN STROMELYSIN-1 / 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-8MI / N-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-PHENYLETHYL)GLYCYL-L-ARGININE-N-PHENYLAMIDE


Mass: 483.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N6O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

NMR software
NameDeveloperClassification
DIANAGUNTERT,BRAUN,WUTHRICHrefinement
FANTOMVON FREYBERG,SCHAUMANN,BRAUNrefinement
NMR ensembleConformers submitted total number: 30

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