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- PDB-5lvd: Thermolysin in complex with inhibitor (JC67) -

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Basic information

Entry
Database: PDB / ID: 5lvd
TitleThermolysin in complex with inhibitor (JC67)
ComponentsThermolysin
KeywordsHYDROLASE / METALLOPROTEASE / 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
Chem-79F / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKrimmer, S.G. / Cramer, J. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind Germany
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin.
Authors: Krimmer, S.G. / Cramer, J. / Schiebel, J. / Heine, A. / Klebe, G.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)35,37211
Polymers34,3601
Non-polymers1,01210
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-49 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.846, 92.846, 130.426
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
11E-779-

HOH

21E-806-

HOH

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 233-548 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 396 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-79F / (2~{S})-4-methyl-2-[[(2~{S})-3-oxidanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]pentanoic acid


Mass: 445.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28N3O8P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO DOUBLE CRYSTAL MONOCHROMATOR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 91830 / % possible obs: 99.9 % / Redundancy: 24.86 % / Rsym value: 0.066 / Net I/σ(I): 35.16
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 24.72 % / Rmerge(I) obs: 0.495 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8TLN

8tln


Resolution: 1.25→38.243 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 8.98
RfactorNum. reflection% reflection
Rfree0.1248 4591 5 %
Rwork0.105 --
obs0.106 91823 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→38.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 55 386 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092676
X-RAY DIFFRACTIONf_angle_d1.123669
X-RAY DIFFRACTIONf_dihedral_angle_d18.154923
X-RAY DIFFRACTIONf_chiral_restr0.089388
X-RAY DIFFRACTIONf_plane_restr0.008492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2493-1.26350.14761450.11562758X-RAY DIFFRACTION97
1.2635-1.27830.1551510.10732871X-RAY DIFFRACTION100
1.2783-1.29390.13391520.10212881X-RAY DIFFRACTION100
1.2939-1.31030.1291500.10182854X-RAY DIFFRACTION100
1.3103-1.32750.14941510.09742873X-RAY DIFFRACTION100
1.3275-1.34570.1431510.09582863X-RAY DIFFRACTION100
1.3457-1.36490.11671510.09192867X-RAY DIFFRACTION100
1.3649-1.38530.1051520.09312884X-RAY DIFFRACTION100
1.3853-1.4070.13431500.08982864X-RAY DIFFRACTION100
1.407-1.430.12491520.09052872X-RAY DIFFRACTION100
1.43-1.45470.10991510.08552877X-RAY DIFFRACTION100
1.4547-1.48120.1171510.08062872X-RAY DIFFRACTION100
1.4812-1.50960.1041520.08272890X-RAY DIFFRACTION100
1.5096-1.54050.11421520.08082874X-RAY DIFFRACTION100
1.5405-1.5740.1061520.08012895X-RAY DIFFRACTION100
1.574-1.61060.11751520.0842886X-RAY DIFFRACTION100
1.6106-1.65080.10191520.08242885X-RAY DIFFRACTION100
1.6508-1.69550.12171520.08842902X-RAY DIFFRACTION100
1.6955-1.74540.11681530.09032896X-RAY DIFFRACTION100
1.7454-1.80170.11141530.09112904X-RAY DIFFRACTION100
1.8017-1.86610.11081530.09572917X-RAY DIFFRACTION100
1.8661-1.94080.1211530.09742906X-RAY DIFFRACTION100
1.9408-2.02910.12221540.10052923X-RAY DIFFRACTION100
2.0291-2.13610.09841540.10082930X-RAY DIFFRACTION100
2.1361-2.26990.11531550.10192936X-RAY DIFFRACTION100
2.2699-2.44520.12651550.10432958X-RAY DIFFRACTION100
2.4452-2.69120.12381550.10892946X-RAY DIFFRACTION100
2.6912-3.08040.12281580.11763002X-RAY DIFFRACTION100
3.0804-3.88040.14971600.12393028X-RAY DIFFRACTION100
3.8804-38.2610.14061690.13463218X-RAY DIFFRACTION100

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