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- PDB-3tmn: THE BINDING OF L-VALYL-L-TRYPTOPHAN TO CRYSTALLINE THERMOLYSIN IL... -

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Entry
Database: PDB / ID: 3tmn
TitleTHE BINDING OF L-VALYL-L-TRYPTOPHAN TO CRYSTALLINE THERMOLYSIN ILLUSTRATES THE MODE OF INTERACTION OF A PRODUCT OF PEPTIDE HYDROLYSIS
ComponentsTHERMOLYSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / 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 ...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
TRYPTOPHAN / VALINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR SUPSTATUTION / Resolution: 1.7 Å
AuthorsHolden, H.M. / Matthews, B.W.
Citation
Journal: J.Biol.Chem. / Year: 1988
Title: The binding of L-valyl-L-tryptophan to crystalline thermolysin illustrates the mode of interaction of a product of peptide hydrolysis.
Authors: Holden, H.M. / 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: Binding of N-Carboxymethyl Dipepetide 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.
#4: 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.
#5: 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.
#6: 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.
#7: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution
Authors: Holmes, M.A. / Matthews, B.W.
#8: 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.
#9: 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.
#10: Journal: J.Biol.Chem. / Year: 1977
Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin
Authors: Kester, W.R. / Matthews, B.W.
#11: 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.
#12: 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.
#13: Journal: Biochemistry / Year: 1976
Title: Role of Calcium in the Thermal Stability of Thermolysin
Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L.
#14: 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.
#15: 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.
#16: Journal: J.Biol.Chem. / Year: 1974
Title: The Conformation of Thermolysin
Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R.
#17: Journal: Biochemistry / Year: 1974
Title: Binding of Lanthanide Ions to Thermolysin
Authors: Matthews, B.W. / Weaver, L.H.
#18: 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.
#19: 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.
#20: 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.
#21: 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.
#22: Journal: Macromolecules / Year: 1972
Title: The Gamma Turn. Evidence for a New Folded Conformation in Proteins
Authors: Matthews, B.W.
#23: 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 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_torsion / struct_conn / struct_conn_type
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_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_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 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)34,9098
Polymers34,3621
Non-polymers5477
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.100, 94.100, 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 2616 - 2618 LIE IN SUBSITE S1(PRIME). / 3: ATOMS 2623 - 2632 LIE IN SUBSITE S2(PRIME).

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Components

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Protein , 1 types, 1 molecules E

#1: Protein THERMOLYSIN


Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 5 types, 180 molecules

#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ACTIVE SITE CLEFT OF THERMOLYSIN CONTAINS AT LEAST FOUR SUBSITES S1, S1(PRIME), S2, AND ...THE ACTIVE SITE CLEFT OF THERMOLYSIN CONTAINS AT LEAST FOUR SUBSITES S1, S1(PRIME), S2, AND S2(PRIME) WHICH PARTICIPATE IN THE BINDING OF EXTENDED SUBSTRATES. THEY ARE SPECIFIED ON *SITE* RECORDS BELOW.
Nonpolymer detailsTHE DIPEPTIDE VAL-TRP IS PRODUCT OF MERCAPTOACETYL-L-VALYL-L-TRYPTOPHAN HYDROLYZED BY THERMOLYSIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMcalcium acetate11
210 mMTris11
37 %(v/v)dimethylsulfoxide11

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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: 1988
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→29.8 Å / Num. obs: 28779 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.049 / Rsym value: 0.031
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 28779 / Num. measured all: 45350 / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
TNTrefinement
OSCTSTdata reduction
AGROVATA/ROTAVATEdata scaling
FRODOmodel building
RefinementMethod to determine structure: MOLECULAR SUPSTATUTION / Resolution: 1.7→10 Å / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: TNT PROTGEO VERSION 1.0 /
RfactorNum. reflection
all0.173 28604
obs0.173 28604
Solvent computationSolvent model: NONE
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 27 173 2632
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg3.2
X-RAY DIFFRACTIONt_dihedral_angle_d16.60
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle0
X-RAY DIFFRACTIONt_trig_c_planes0.011
X-RAY DIFFRACTIONt_gen_planes0.017
X-RAY DIFFRACTIONt_it0
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Num. reflection obs: 28604
Solvent computation
*PLUS
Displacement parameters
*PLUS

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