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- PDB-5tln: BINDING OF HYDROXAMIC ACID INHIBITORS TO CRYSTALLINE THERMOLYSIN ... -

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Entry
Database: PDB / ID: 5tln
TitleBINDING OF HYDROXAMIC ACID INHIBITORS TO CRYSTALLINE THERMOLYSIN SUGGESTS A PENTACOORDINATE ZINC INTERMEDIATE IN CATALYSIS
ComponentsTHERMOLYSIN
KeywordsHYDROLASE (METALLOPROTEINASE)
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 ...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
HONH-BENZYLMALONYL-L-ALANYLGLYCINE-P-NITROANILIDE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR SUBSTATUTION / Resolution: 2.3 Å
AuthorsMatthews, B.W. / Holmes, M.A.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution
Authors: Holmes, M.A. / Matthews, B.W.
#2: 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.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 1977
Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin
Authors: Kester, W.R. / Matthews, B.W.
#5: 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.
#6: 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.
#7: Journal: Biochemistry / Year: 1976
Title: Role of Calcium in the Thermal Stability of Thermolysin
Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L.
#8: 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.
#9: Journal: J.Biol.Chem. / Year: 1974
Title: The Conformation of Thermolysin
Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R.
#10: Journal: Biochemistry / Year: 1974
Title: Binding of Lanthanide Ions to Thermolysin
Authors: Matthews, B.W. / Weaver, L.H.
#11: 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.
#12: 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.
#13: 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.
#14: 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.
#15: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionFeb 8, 1982Processing site: BNL
Revision 1.0May 26, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
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_rmsd_angle / pdbx_validate_rmsd_bond / 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][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _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 / _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
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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
A: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0457
Polymers34,3621
Non-polymers6836
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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: HET GROUP INA IS HONH-BENZYLMALONYL-L-ALANYLGLYCINE-P-NITROANILIDE. NO COORDINATES FOR THE P-NITROANILIDE GROUP ARE INCLUDED IN THIS ENTRY BECAUSE IT APPEARED TO ASSUME SO MANY CONFORMATIONS THAT ...2: HET GROUP INA IS HONH-BENZYLMALONYL-L-ALANYLGLYCINE-P-NITROANILIDE. NO COORDINATES FOR THE P-NITROANILIDE GROUP ARE INCLUDED IN THIS ENTRY BECAUSE IT APPEARED TO ASSUME SO MANY CONFORMATIONS THAT THERE WAS NO DENSITY FOR IT IN THE MAP.

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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)
References: UniProt: P00800, thermolysin
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BAN / HONH-BENZYLMALONYL-L-ALANYLGLYCINE-P-NITROANILIDE


Mass: 457.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.45 Å3/Da / Density % sol: 49.76 % / Description: data collected with precession photography
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
35 %(v/v)dimethylsulfoxide11

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-3 / Wavelength: 1.54
DetectorType: KODAK / Detector: FILM / Date: 1980 / Details: ADJUSTABLE COLLIMATOR SLIT
RadiationMonochromator: NICKEL FILTER / Protocol: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→22.6 Å / Num. obs: 11989 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.021 / Rsym value: 0.065
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 11989 / Rmerge(I) obs: 0.021

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Processing

Software
NameClassification
TNTrefinement
VENUSdata reduction
ODPROCdata scaling
PROLSQrefinement
RefinementMethod to determine structure: MOLECULAR SUBSTATUTION / Resolution: 2.3→10 Å / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: TNT PROTGEO VERSION 1.0 /
RfactorNum. reflection
all0.179 11797
obs0.179 11797
Solvent computationSolvent model: NONE
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 28 146 2606
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0472514
X-RAY DIFFRACTIONt_angle_deg6.13410
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle0
X-RAY DIFFRACTIONt_trig_c_planes0.00766
X-RAY DIFFRACTIONt_gen_planes0.012378
X-RAY DIFFRACTIONt_it0
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 11797
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.047
X-RAY DIFFRACTIONo_angle_deg6.1

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