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- PDB-1thl: Thermolysin complexed with a novel glutaramide derivative, n-(1-(... -

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Basic information

Entry
Database: PDB / ID: 1thl
TitleThermolysin complexed with a novel glutaramide derivative, n-(1-(2(r,s)-carboxy-4-phenylbutyl) cyclopentylcarbonyl)-(s)-tryptophan
ComponentsTHERMOLYSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEINASE / GLUTARAMIDE DERIVATIVE / THERMOLYSIN / 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
N-({1-[(2S)-2-carboxy-4-phenylbutyl]cyclopentyl}carbonyl)-L-tryptophan / Chem-0DB / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsHolland, D.R. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1994
Title: Inhibition of Thermolysin and Neutral Endopeptidase 24.11 By a Novel Glutaramide Derivative; X-Ray Structure Determination of the Thermolysin-Inhibitor Complex
Authors: Holland, D.R. / Barclay, P.L. / Danilewicz, J.C. / Matthews, B.W. / James, K.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution
Authors: Holmes, M.A. / Matthews, B.W.
#3: Journal: J.Biol.Chem. / Year: 1974
Title: The Conformation of Thermolysin
Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R.
#4: 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. / Neura, H.
#5: Journal: Nature New Biol. / Year: 1972
Title: Three Dimensional Structure of Thermolysin
Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.N. / Schoenborn, B.P. / Duporque, D.
History
DepositionNov 17, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)35,0657
Polymers34,3621
Non-polymers7026
Water2,666148
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: CIS PROLINE - PRO 51

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Components

#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
#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-0DB / N-({1-[(2S)-2-carboxy-4-phenylbutyl]cyclopentyl}carbonyl)-L-tryptophan / CCT


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 476.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H32N2O5
References: N-({1-[(2S)-2-carboxy-4-phenylbutyl]cyclopentyl}carbonyl)-L-tryptophan
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DENSITY AT POSITION 177 CLEARLY SHOWS RESIDUE GLU, NOT LYS. AUTHORS MAINTAIN THAT THE SWISSPROT ...THE DENSITY AT POSITION 177 CLEARLY SHOWS RESIDUE GLU, NOT LYS. AUTHORS MAINTAIN THAT THE SWISSPROT REFERENCE P00800 IS LIKELY TO BE INCORRECT AT THIS POSITION

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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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / pH: 7.2
Details: TRIS ACETATE, CALCIUM ACETATE, DMSO, PH 7.2, DILUTION WITH H2O, TEMPERATURE 277K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1991 / Details: GRAPHITE MONOCHROMATOR, COLLIMATING SLITS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→35 Å / Num. obs: 41090 / % possible obs: 86 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 34103 / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
Xuong-HamlinAligndata collection
Xuong-HamlinScaling Suitedata reduction
TNTrefinement
XUONG-HAMLIN(DETECTOR SYSTEM)data scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3TLN

3tln
PDB Unreleased entry


Resolution: 1.7→10 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: TNT VERSION 1.0
RfactorNum. reflection% reflection
Rwork0.162 --
all0.162 34103 -
obs0.162 33922 89 %
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 40 148 2620
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0172531
X-RAY DIFFRACTIONt_angle_deg2.5363430
X-RAY DIFFRACTIONt_dihedral_angle_d16.26614430
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01968
X-RAY DIFFRACTIONt_gen_planes0.027377
X-RAY DIFFRACTIONt_it7.15525100
X-RAY DIFFRACTIONt_nbd0.15716
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 33922 / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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