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- PDB-5jss: Thermolysin in complex with JC149. -

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Basic information

Entry
Database: PDB / ID: 5jss
TitleThermolysin in complex with JC149.
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-6NG / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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 9, 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 / 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)35,46012
Polymers34,3601
Non-polymers1,10011
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-48 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.528, 92.528, 131.314
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-781-

HOH

21E-838-

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, 435 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-6NG / N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2R)-2,3,3-trimethylbutyl]-L-leucinamide


Mass: 455.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N3O5P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 47.94 %
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: May 9, 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: 1.19→50 Å / Num. obs: 106247 / % possible obs: 100 % / Redundancy: 15.1 % / Rsym value: 0.095 / Net I/σ(I): 18.18
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 15 % / Mean I/σ(I) obs: 5.17 / % possible all: 99.7

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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: 1.19→40.066 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 8.64
RfactorNum. reflection% reflection
Rfree0.1209 5312 5 %
Rwork0.1034 --
obs0.1043 106241 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.19→40.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 60 424 2900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112615
X-RAY DIFFRACTIONf_angle_d1.1613575
X-RAY DIFFRACTIONf_dihedral_angle_d21.927915
X-RAY DIFFRACTIONf_chiral_restr0.097379
X-RAY DIFFRACTIONf_plane_restr0.009469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1893-1.20280.15271720.12053265X-RAY DIFFRACTION99
1.2028-1.21690.14981750.11763327X-RAY DIFFRACTION100
1.2169-1.23180.14791740.11033300X-RAY DIFFRACTION100
1.2318-1.24740.12511750.10643319X-RAY DIFFRACTION100
1.2474-1.26380.11471750.10153336X-RAY DIFFRACTION100
1.2638-1.28110.1281740.09893310X-RAY DIFFRACTION100
1.2811-1.29940.10561740.09683295X-RAY DIFFRACTION100
1.2994-1.31880.12771750.09733337X-RAY DIFFRACTION100
1.3188-1.33940.10581760.09533331X-RAY DIFFRACTION100
1.3394-1.36140.11831750.09483327X-RAY DIFFRACTION100
1.3614-1.38490.11121750.08743331X-RAY DIFFRACTION100
1.3849-1.410.1051750.08823326X-RAY DIFFRACTION100
1.41-1.43720.10991750.08953323X-RAY DIFFRACTION100
1.4372-1.46650.10531750.08723331X-RAY DIFFRACTION100
1.4665-1.49840.12021760.08383336X-RAY DIFFRACTION100
1.4984-1.53320.09511760.08373343X-RAY DIFFRACTION100
1.5332-1.57160.10931770.08133358X-RAY DIFFRACTION100
1.5716-1.61410.09821750.0853328X-RAY DIFFRACTION100
1.6141-1.66160.11091770.08373357X-RAY DIFFRACTION100
1.6616-1.71520.10591770.08893367X-RAY DIFFRACTION100
1.7152-1.77650.10821770.08933367X-RAY DIFFRACTION100
1.7765-1.84760.11851770.09273368X-RAY DIFFRACTION100
1.8476-1.93170.12151780.09633381X-RAY DIFFRACTION100
1.9317-2.03360.11231780.09763372X-RAY DIFFRACTION100
2.0336-2.1610.10421780.09493394X-RAY DIFFRACTION100
2.161-2.32780.11441800.10013412X-RAY DIFFRACTION100
2.3278-2.5620.12691800.10283431X-RAY DIFFRACTION100
2.562-2.93270.12161820.10743443X-RAY DIFFRACTION100
2.9327-3.69440.13611840.11713513X-RAY DIFFRACTION100
3.6944-40.08850.14251950.13973701X-RAY DIFFRACTION100

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