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- PDB-1pe7: Thermolysin with bicyclic inhibitor -

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Basic information

Entry
Database: PDB / ID: 1pe7
TitleThermolysin with bicyclic inhibitor
ComponentsThermolysin
KeywordsHYDROLASE / METALLOPROTEASE
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
2-(4-METHYLPHENOXY)ETHYLPHOSPHINATE / 3-METHYLBUTAN-1-AMINE / LEUCINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsJuers, D. / Yusuff, N. / Bartlett, P.A. / Matthews, B.W.
Citation
Journal: To be Published
Title: Conformational Constraint and Structural Complementarity in Thermolysin Inhibitors: Structures of Enzyme Complexes and Conclusions
Authors: Bartlett, P.A. / Yusuff, N. / Lindval, M.K. / Holland, D. / Juers, D. / Matthews, B.W.
#1: Journal: J.Am.Chem.Soc. / Year: 1994
Title: Structure-Based Design of an Inhibitor of the Zinc Peptidase Thermolysin
Authors: Morgan, B.P. / Holland, D. / Matthews, B.W. / Bartlett, P.A.
History
DepositionMay 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)35,08410
Polymers34,3621
Non-polymers7219
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.800, 93.800, 131.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-619-

HOH

21A-690-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 , 7 types, 202 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-4BR / 2-(4-METHYLPHENOXY)ETHYLPHOSPHINATE


Mass: 199.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O3P
#5: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Chemical ChemComp-LEN / 3-METHYLBUTAN-1-AMINE


Type: L-peptide COOH carboxy terminus / Mass: 87.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13N
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.82→38.17 Å / Num. all: 28471 / Num. obs: 29471 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.4
Reflection shellResolution: 1.82→1.96 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3620 / % possible all: 59

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
TNTrefinement
SDMSdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→20 Å / σ(F): 0 / Stereochemistry target values: TNT
Details: ACCORDING TO THE AUTHOR, SOME ATOMS WITH ALTERNATE CONFORMATIONS WERE NOT RESTRAINED DURING REFINEMENT. THEREFORE THEIR OCCUPANCIES MAY BE GREATER THAN 1.0. Only one conformation is given ...Details: ACCORDING TO THE AUTHOR, SOME ATOMS WITH ALTERNATE CONFORMATIONS WERE NOT RESTRAINED DURING REFINEMENT. THEREFORE THEIR OCCUPANCIES MAY BE GREATER THAN 1.0. Only one conformation is given each for Leucine 202 and the neighboring isobutyl side chain of the inhibitor (residue LEN 324), although the electron density suggests multiple conformations. However, in both cases the conformation given appears to be the dominant one. (With the isobutyl side chain, the ambiguity is with regard to Chi2. With Leu 202 the ambiguity is also with Chi2 and to a lesser degree with Chi1.)
RfactorNum. reflection
all0.139 28433
obs0.139 28433
Refinement stepCycle: LAST / Resolution: 1.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 36 193 2679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_bond_d0.017

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