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- PDB-1tmn: Binding of n-carboxymethyl dipeptide inhibitors to thermolysin de... -

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Entry
Database: PDB / ID: 1tmn
TitleBinding of n-carboxymethyl dipeptide inhibitors to thermolysin determined by x-ray crystallography. a novel class of transition-state analogues for zinc peptidases
ComponentsTHERMOLYSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-[(1S)-1-carboxy-3-phenylpropyl]-L-leucyl-L-tryptophan / Chem-0ZN / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR SUBSTATUTION / Resolution: 1.9 Å
AuthorsMonzingo, A.F. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1984
Title: Binding of N-carboxymethyl dipeptide inhibitors to thermolysin determined by X-ray crystallography: a novel class of transition-state analogues for zinc peptidases
Authors: Monzingo, A.F. / Matthews, B.W.
#1: Journal: Science / Year: 1987
Title: Structures of Two Thermolysin-Inhibitor Complexes that Differ by a Single Hydrogen Bond
Authors: Tronrud, D.E. / Holden, H.M. / Matthews, B.W.
#2: Journal: Eur.J.Biochem. / Year: 1986
Title: Crystallographic Structural Analysis of Phosphoramidates as Inhibitors and Transition-State Analogs of Thermolysin
Authors: Tronrud, D.E. / Monzingo, A.F. / Matthews, B.W.
#3: Journal: Biochemistry / Year: 1984
Title: An Interactive Computer Graphics Study of Thermolysin-Catalyzed Peptide Cleavage and Inhibition by N-Carboxymethyl Dipeptides
Authors: Hangauer, D.G. / Monzingo, A.F. / Matthews, B.W.
#4: Journal: Biochemistry / Year: 1983
Title: Structural Analysis of the Inhibition of Thermolysin by an Active-Site-Directed Irreversible Inhibitor
Authors: Holmes, M.A. / Tronrud, D.E. / Matthews, B.W.
#5: Journal: Biochemistry / Year: 1982
Title: Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans
Authors: Monzingo, A.F. / Matthews, B.W.
#6: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution
Authors: Holmes, M.A. / Matthews, B.W.
#7: Journal: Biochemistry / Year: 1981
Title: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis
Authors: Holmes, M.A. / Matthews, B.W.
#8: Journal: J.Biol.Chem. / Year: 1979
Title: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography
Authors: Bolognesi, M.C. / Matthews, B.W.
#9: Journal: J.Biol.Chem. / Year: 1977
Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin
Authors: Kester, W.R. / Matthews, B.W.
#10: Journal: J.Mol.Biol. / Year: 1977
Title: A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates
Authors: Weaver, L.H. / Kester, W.R. / Matthews, B.W.
#11: Journal: Biochemistry / Year: 1977
Title: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis
Authors: Kester, W.R. / Matthews, B.W.
#12: Journal: Biochemistry / Year: 1976
Title: Role of Calcium in the Thermal Stability of Thermolysin
Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L.
#13: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis
Authors: Levy, P.L. / Pangburn, M.K. / Burstein, Y. / Ericsson, L.H. / Neurath, H. / Walsh, K.A.
#14: Journal: Experientia,Suppl. / Year: 1976
Title: The Structure and Stability of Thermolysin
Authors: Weaver, L.H. / Kester, W.R. / Teneyck, L.F. / Matthews, B.W.
#15: Journal: J.Biol.Chem. / Year: 1974
Title: The Conformation of Thermolysin
Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R.
#16: Journal: Biochemistry / Year: 1974
Title: Binding of Lanthanide Ions to Thermolysin
Authors: Matthews, B.W. / Weaver, L.H.
#17: Journal: J.Mol.Biol. / Year: 1972
Title: The Structure of Thermolysin. An Electron Density Map at 2.3 Angstroms Resolution
Authors: Colman, P.M. / Jansonius, J.N. / Matthews, B.W.
#18: Journal: Nature New Biol. / Year: 1972
Title: Amino-Acid Sequence of Thermolysin
Authors: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H.
#19: Journal: Nature New Biol. / Year: 1972
Title: Three Dimensional Structure of Thermolysin
Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D.
#20: Journal: Nature New Biol. / Year: 1972
Title: Structure of Thermolysin
Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H.
#21: Journal: Macromolecules / Year: 1972
Title: The Gamma Turn. Evidence for a New Folded Conformation in Proteins
Authors: Matthews, B.W.
#22: Journal: Biochem.Biophys.Res.Commun. / Year: 1972
Title: Rare Earths as Isomorphous Calcium Replacements for Protein Crystallography
Authors: Colman, P.M. / Weaver, L.H. / Matthews, B.W.
History
DepositionJun 29, 1987Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 23, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _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 / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_symm_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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
Details: ORTHOGONAL X,Y,Z AXES WERE REALIGNED FROM A*,B,C TO A,B*,C CRYSTALLOGRAPHIC DIRECTIONS
Provider: repository / Type: Remediation
Remark 650HELIX TURNS 14, 20 AND 21 OF TABLE VIII IN THE PAPER CITED AS REFERENCE 10 ABOVE WERE NOT INCLUDED ...HELIX TURNS 14, 20 AND 21 OF TABLE VIII IN THE PAPER CITED AS REFERENCE 10 ABOVE WERE NOT INCLUDED IN THE TURN RECORDS BELOW BECAUSE THESE CORRESPOND TO HELICAL SUBSTRUCTURES SPECIFIED IN THE HELIX RECORDS.
Remark 700SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO ...SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO DISTINCT SEQUENCES OF THE POLYPEPTIDE CHAIN. TO REPRESENT THIS FEATURE AN EXTRA SHEET IS DEFINED. STRANDS 2,3,4,5 OF S1 ARE IDENTICAL TO STRANDS 2,3,4,5 OF S2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0687
Polymers34,3621
Non-polymers7056
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.200, 94.200, 131.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: RESIDUE 51 IS A CIS-PROLINE. / 2: ATOMS 2584 - 2591 LIE IN SUBSITE S1. / 3: ATOMS 2599 - 2602 LIE IN SUBSITE S1(PRIME). / 4: ATOMS 2607 - 2616 LIE IN SUBSITE S2(PRIME). / 5: ATOMS 2593 AND 2594 ARE BONDED TO THE ZINC ATOM.
6: THE CHIRALITY AROUND ATOM CB IN RESIDUES ILE E 197 AND THR E 278 IS INCORRECT.

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Components

#1: Protein THERMOLYSIN /


Mass: 34362.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
Gene: npr / References: UniProt: P00800, thermolysin
#2: Chemical ChemComp-0ZN / N-[(1R)-1-carboxy-3-phenylpropyl]-L-leucyl-L-tryptophan


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 479.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N3O5
References: N-[(1S)-1-carboxy-3-phenylpropyl]-L-leucyl-L-tryptophan
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.01 Mcalcium acetate11
20.01 MTris acetate11
37 %(v/v)dimethyl sulfoxide11

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.54
DetectorType: KODAK / Detector: FILM / Date: 1983
RadiationMonochromator: Graphite monochromator / Protocol: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→14.9 Å / Num. obs: 23734 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Rsym value: 0.048
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 23734 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
EREFrefinement
OSCTSTdata reduction
AGROVATA/ROTAVATEdata scaling
RICHARDSBOX MODELINGphasing
RefinementMethod to determine structure: MOLECULAR SUBSTATUTION / Resolution: 1.9→14.9 Å / Cross valid method: NONE / σ(F): 0 /
RfactorNum. reflection
Rwork0.171 -
obs-19842
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 40 144 2616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.021
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.6
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Num. reflection obs: 19842
Solvent computation
*PLUS
Displacement parameters
*PLUS

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