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- PDB-1ums: STROMELYSIN-1 CATALYTIC DOMAIN WITH HYDROPHOBIC INHIBITOR BOUND, ... -

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Entry
Database: PDB / ID: 1ums
TitleSTROMELYSIN-1 CATALYTIC DOMAIN WITH HYDROPHOBIC INHIBITOR BOUND, PH 7.0, 32OC, 20 MM CACL2, 15% ACETONITRILE; NMR ENSEMBLE OF 20 STRUCTURES
ComponentsSTROMELYSIN-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ZINC HYDROLASE / METZINCIN / MATRIX METALLOPROTEINASE / 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 / 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
N-{(2S)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-L-leucyl-L-phenylalaninamide / Chem-0DS / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsVan Doren, S.R. / Kurochkin, A.V. / Hu, W. / Zuiderweg, E.R.P.
Citation
Journal: Protein Sci. / Year: 1995
Title: Solution structure of the catalytic domain of human stromelysin complexed with a hydrophobic inhibitor.
Authors: Van Doren, S.R. / Kurochkin, A.V. / Hu, W. / Ye, Q.Z. / Johnson, L.L. / Hupe, D.J. / Zuiderweg, E.R.
#1: Journal: Biochemistry / Year: 1993
Title: Assignments for the Main-Chain Nuclear Magnetic Resonances and Delineation of the Secondary Structure of the Catalytic Domain of Human Stromelysin-1 as Obtained from Triple-Resonance 3D NMR Experiments
Authors: Van Doren, S.R. / Kurochkin, A.V. / Ye, Q.-Z. / Johnson, L.L. / Hupe, D.J. / Zuiderweg, E.R.P.
History
DepositionOct 31, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Sep 23, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_related / pdbx_database_status ...pdbx_database_related / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _pdbx_database_status.process_site / _pdbx_nmr_software.name ..._pdbx_database_status.process_site / _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_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
Revision 1.5May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,1335
Polymers19,5141
Non-polymers6194
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: CIS PROLINE - PRO A 87 MODEL 1 / 2: CIS PROLINE - PRO A 109 MODEL 1
3: THR A 128 - PRO A 129 MODEL 1 OMEGA = 140.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: TYR A 155 - PRO A 156 MODEL 1 OMEGA = 211.20 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: TYR A 220 - PRO A 221 MODEL 1 OMEGA = 220.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: CIS PROLINE - PRO A 87 MODEL 2
7: THR A 128 - PRO A 129 MODEL 2 OMEGA = 140.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: CIS PROLINE - PRO A 87 MODEL 3
9: THR A 128 - PRO A 129 MODEL 3 OMEGA = 137.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: TYR A 220 - PRO A 221 MODEL 3 OMEGA = 229.78 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: THR A 128 - PRO A 129 MODEL 4 OMEGA = 131.14 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: TYR A 155 - PRO A 156 MODEL 4 OMEGA = 218.19 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: GLY A 159 - PRO A 160 MODEL 4 OMEGA = 222.63 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
14: ALA A 169 - PRO A 170 MODEL 4 OMEGA = 245.06 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
15: CIS PROLINE - PRO A 87 MODEL 5
16: THR A 128 - PRO A 129 MODEL 5 OMEGA = 143.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
17: CIS PROLINE - PRO A 87 MODEL 6
18: THR A 128 - PRO A 129 MODEL 6 OMEGA = 136.67 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
19: TYR A 220 - PRO A 221 MODEL 6 OMEGA = 225.35 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
20: CIS PROLINE - PRO A 87 MODEL 7
21: THR A 128 - PRO A 129 MODEL 7 OMEGA = 141.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
22: CIS PROLINE - PRO A 172 MODEL 7
23: TYR A 220 - PRO A 221 MODEL 7 OMEGA = 229.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
24: CIS PROLINE - PRO A 87 MODEL 8
25: ILE A 89 - PRO A 90 MODEL 8 OMEGA = 223.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
26: THR A 128 - PRO A 129 MODEL 8 OMEGA = 143.14 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
27: GLY A 159 - PRO A 160 MODEL 8 OMEGA = 221.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
28: CIS PROLINE - PRO A 90 MODEL 9 / 29: CIS PROLINE - PRO A 87 MODEL 10
30: THR A 128 - PRO A 129 MODEL 10 OMEGA = 137.84 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
31: CIS PROLINE - PRO A 87 MODEL 11
32: ILE A 89 - PRO A 90 MODEL 11 OMEGA = 148.36 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
33: THR A 128 - PRO A 129 MODEL 11 OMEGA = 143.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
34: CIS PROLINE - PRO A 87 MODEL 12
35: THR A 128 - PRO A 129 MODEL 12 OMEGA = 141.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
36: GLY A 159 - PRO A 160 MODEL 12 OMEGA = 214.44 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
37: CIS PROLINE - PRO A 87 MODEL 13
38: THR A 128 - PRO A 129 MODEL 13 OMEGA = 139.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
39: TYR A 155 - PRO A 156 MODEL 13 OMEGA = 255.71 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
40: ALA A 169 - PRO A 170 MODEL 13 OMEGA = 305.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
41: TYR A 220 - PRO A 221 MODEL 13 OMEGA = 221.23 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
42: CIS PROLINE - PRO A 87 MODEL 14
43: THR A 128 - PRO A 129 MODEL 14 OMEGA = 137.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
44: TYR A 220 - PRO A 221 MODEL 14 OMEGA = 225.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
45: CIS PROLINE - PRO A 87 MODEL 15
46: THR A 128 - PRO A 129 MODEL 15 OMEGA = 142.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
47: CIS PROLINE - PRO A 87 MODEL 16
48: THR A 128 - PRO A 129 MODEL 16 OMEGA = 141.90 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
49: TYR A 155 - PRO A 156 MODEL 16 OMEGA = 256.07 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
50: CIS PROLINE - PRO A 87 MODEL 17
51: ILE A 89 - PRO A 90 MODEL 17 OMEGA = 239.90 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
52: THR A 128 - PRO A 129 MODEL 17 OMEGA = 139.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
53: CIS PROLINE - PRO A 172 MODEL 17 / 54: CIS PROLINE - PRO A 87 MODEL 18
55: THR A 128 - PRO A 129 MODEL 18 OMEGA = 137.94 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
56: CIS PROLINE - PRO A 156 MODEL 18
57: ALA A 169 - PRO A 170 MODEL 18 OMEGA = 319.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
58: CIS PROLINE - PRO A 172 MODEL 18
59: TYR A 220 - PRO A 221 MODEL 18 OMEGA = 235.68 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
60: CIS PROLINE - PRO A 87 MODEL 19
61: THR A 105 - PRO A 106 MODEL 19 OMEGA = 211.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
62: THR A 128 - PRO A 129 MODEL 19 OMEGA = 142.69 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
63: TYR A 155 - PRO A 156 MODEL 19 OMEGA = 243.41 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
64: CIS PROLINE - PRO A 87 MODEL 20
65: THR A 128 - PRO A 129 MODEL 20 OMEGA = 128.85 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
66: TYR A 220 - PRO A 221 MODEL 20 OMEGA = 230.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein STROMELYSIN-1 / MATRIX METALLOPROTEINASE-3 / MMP-3


Mass: 19513.646 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 83 - 256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: INDUCTION BY M13 WITH T7 RNA POLYMERASE / Gene: HUMAN STROMELYSIN-1 CATALYTIC / Plasmid: PGEMEX-D
Gene (production host): HUMAN STROMELYSIN-1 CATALYTIC DOMAIN
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.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-0DS / N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-L-leucyl-L-phenylalaninamide / ICI U24522


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 448.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36N4O5
References: N-{(2S)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-L-leucyl-L-phenylalaninamide

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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
DGIIHAVELrefinement
DiscoverBIOSYM TECHNOLOGIES, INC.refinement
NMR ensembleConformers submitted total number: 20

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