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- PDB-1hfs: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STR... -

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Entry
Database: PDB / ID: 1hfs
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE N-CARBOXY-ALKYL INHIBITOR L-764,004
ComponentsSTROMELYSIN-1
KeywordsHYDROLASE / METALLOPROTEASE / MATRIX METALLOPROTEASE-3 / PROTEOGLYCANASE
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-L04 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBecker, J.W.
Citation
Journal: J.Med.Chem. / Year: 1997
Title: Inhibition of stromelysin-1 (MMP-3) by P1'-biphenylylethyl carboxyalkyl dipeptides.
Authors: Esser, C.K. / Bugianesi, R.L. / Caldwell, C.G. / Chapman, K.T. / Durette, P.L. / Girotra, N.N. / Kopka, I.E. / Lanza, T.J. / Levorse, D.A. / MacCoss, M. / Owens, K.A. / Ponpipom, M.M. / ...Authors: Esser, C.K. / Bugianesi, R.L. / Caldwell, C.G. / Chapman, K.T. / Durette, P.L. / Girotra, N.N. / Kopka, I.E. / Lanza, T.J. / Levorse, D.A. / MacCoss, M. / Owens, K.A. / Ponpipom, M.M. / Simeone, J.P. / Harrison, R.K. / Niedzwiecki, L. / Becker, J.W. / Marcy, A.I. / Axel, M.G. / Christen, A.J. / McDonnell, J. / Moore, V.L. / Olszewski, J.M. / Saphos, C. / Visco, D.M. / Shen, F. / Colletti, A. / Krieter, P.A. / Hagmann, W.K.
#1: Journal: J.Biomol.NMR / Year: 1996
Title: Comparison of the Structure of Human Recombinant Short Form Stromelysin by Multidimensional Heteronuclear NMR and X-Ray Crystallography
Authors: Gooley, P.R. / O'Connell, J.F. / Marcy, A.I. / Cuca, G.C. / Axel, M.G. / Caldwell, C.G. / Hagmann, W.K. / Becker, J.W.
#2: Journal: Protein Sci. / Year: 1995
Title: Stromelysin-1: Three-Dimensional Structure of the Inhibited Catalytic Domain and of the C-Truncated Proenzyme
Authors: Becker, J.W. / Marcy, A.I. / Rokosz, L.L. / Axel, M.G. / Burbaum, J.J. / Fitzgerald, P.M. / Cameron, P.M. / Esser, C.K. / Hagmann, W.K. / Hermes, J.D. / Springer, J.P.
#3: 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.
#4: Journal: J.Med.Chem. / Year: 1993
Title: Inhibition of Matrix Metalloproteinases by N-Carboxyalkyl Peptides
Authors: Chapman, K.T. / Kopka, I.E. / Durette, P.L. / Esser, C.K. / Lanza, T.J. / Izquierdo-Martin, M. / Niedzwiecki, L. / Chang, B. / Harrison, R.K. / Kuo, D.W. / Lin, T.Y. / Stein, R.L. / Hagmann, W.K.
#5: Journal: Biochemistry / Year: 1991
Title: Human Fibroblast Stromelysin Catalytic Domain: Expression, Purification, and Characterization of a C-Terminally Truncated Form
Authors: Marcy, A.I. / Eiberger, L.L. / Harrison, R. / Chan, H.K. / Hutchinson, N.I. / Hagmann, W.K. / Cameron, P.M. / Boulton, D.A. / Hermes, J.D.
History
DepositionFeb 13, 1997Processing site: BNL
Revision 1.0Feb 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_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.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)18,9037
Polymers17,9461
Non-polymers9576
Water2,576143
1
A: STROMELYSIN-1
hetero molecules

A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,80614
Polymers35,8922
Non-polymers1,91412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)84.140, 85.350, 55.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21A-468-

HOH

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Components

#1: Protein STROMELYSIN-1 / MATRIX METALLOPROTEASE-3 / PROTEOGLYCANASE


Mass: 17945.922 Da / Num. of mol.: 1
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
#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.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-L04 / 6-(4'-FLUORO-BIPHENYL-4-YL)-4-(3-METHYL-1-PHENYLCARBAMOYL-BUTYLCARBAMOYL)-2-[4-(1-OXO-1,3-DIHYDRO-ISOINDOL-2-YL)-BUTYL]-HEXANOIC ACID / L004


Mass: 705.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H48FN3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 53 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116.5 mg/mlprotein1drop
21.2 ML-764,0041drop
35.0 mM1dropCaCl2
40.02 %1dropNaN3
520 mMMES1drop
610 %PEG60001reservoir
75 %sat1reservoirNH4Cl
80.02 %1reservoirNaN3
90.1 Mcacodylate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 29, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21587 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.17 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.0338

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.217 985 4.8 %RANDOM
Rwork0.189 ---
obs0.189 20353 91.5 %-
Displacement parametersBiso mean: 21.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-20 Å
Luzzati sigma a0.08 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 57 143 1471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.31.5
X-RAY DIFFRACTIONx_mcangle_it2.22
X-RAY DIFFRACTIONx_scbond_it2.342
X-RAY DIFFRACTIONx_scangle_it3.642.5
LS refinement shellResolution: 1.7→1.73 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 35 4.2 %
Rwork0.339 800 -
obs--76 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1SLN004.PARSLN004.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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