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- PDB-5js3: Thermolysin in complex with JC114. -

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Basic information

Entry
Database: PDB / ID: 5js3
TitleThermolysin in complex with JC114.
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 / 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
Chem-6MG / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsKrimmer, S.G. / Cramer, J. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind Germany
CitationJournal: J. Med. Chem. / Year: 2016
Title: Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands.
Authors: Krimmer, S.G. / Cramer, J. / Betz, M. / Fridh, V. / Karlsson, R. / Heine, A. / Klebe, G.
History
DepositionMay 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / 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

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,46012
Polymers34,3601
Non-polymers1,10011
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-48 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.616, 92.616, 131.463
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-794-

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 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 439 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 / Glycerol


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


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-6MG / N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-2,3,3-trimethylbutyl]-L-leucinamide


Mass: 455.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N3O5P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7.5 / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO

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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: Aug 7, 2014
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: 1.16→50 Å / Num. obs: 114612 / % possible obs: 99.5 % / Redundancy: 16.08 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.54
Reflection shellResolution: 1.16→1.23 Å / Redundancy: 15.38 % / Rmerge(I) obs: 0.447 / % possible all: 98.3

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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: 1.16→40.104 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 8.69
RfactorNum. reflection% reflection
Rfree0.1236 5731 5 %
Rwork0.1032 --
obs0.1042 114611 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.16→40.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 60 428 2907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012618
X-RAY DIFFRACTIONf_angle_d1.193579
X-RAY DIFFRACTIONf_dihedral_angle_d17.505917
X-RAY DIFFRACTIONf_chiral_restr0.238378
X-RAY DIFFRACTIONf_plane_restr0.009470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1586-1.17170.14931800.1163430X-RAY DIFFRACTION96
1.1717-1.18550.11681870.11013547X-RAY DIFFRACTION99
1.1855-1.20.14531870.10513553X-RAY DIFFRACTION99
1.2-1.21520.131870.10723542X-RAY DIFFRACTION99
1.2152-1.23120.13031870.10383570X-RAY DIFFRACTION99
1.2312-1.2480.13511890.10243581X-RAY DIFFRACTION99
1.248-1.26590.12071880.09993567X-RAY DIFFRACTION99
1.2659-1.28480.1331880.09693576X-RAY DIFFRACTION99
1.2848-1.30480.12421890.09313591X-RAY DIFFRACTION99
1.3048-1.32620.11491880.09213568X-RAY DIFFRACTION100
1.3262-1.34910.10931890.09083593X-RAY DIFFRACTION100
1.3491-1.37360.11551890.08763594X-RAY DIFFRACTION100
1.3736-1.40010.11431900.08843605X-RAY DIFFRACTION100
1.4001-1.42860.1121900.08523613X-RAY DIFFRACTION100
1.4286-1.45970.10121890.08293600X-RAY DIFFRACTION100
1.4597-1.49370.11441910.08223626X-RAY DIFFRACTION100
1.4937-1.5310.11461900.0843601X-RAY DIFFRACTION100
1.531-1.57240.11311910.08223629X-RAY DIFFRACTION100
1.5724-1.61870.1221900.08443612X-RAY DIFFRACTION100
1.6187-1.67090.11021920.08713652X-RAY DIFFRACTION100
1.6709-1.73070.11271920.09053643X-RAY DIFFRACTION100
1.7307-1.79990.11811910.09343637X-RAY DIFFRACTION100
1.7999-1.88190.10781930.09513666X-RAY DIFFRACTION100
1.8819-1.98110.11341930.09713668X-RAY DIFFRACTION100
1.9811-2.10520.10721940.10033684X-RAY DIFFRACTION100
2.1052-2.26770.10731940.10013686X-RAY DIFFRACTION100
2.2677-2.49590.1211960.10413721X-RAY DIFFRACTION100
2.4959-2.8570.12491960.10833722X-RAY DIFFRACTION100
2.857-3.59910.13882000.11583797X-RAY DIFFRACTION100
3.5991-40.12790.14962110.13394006X-RAY DIFFRACTION100

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