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- PDB-5mnr: Thermolysin in complex with inhibitor JC256 -

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Basic information

Entry
Database: PDB / ID: 5mnr
TitleThermolysin in complex with inhibitor JC256
ComponentsThermolysin
KeywordsHYDROLASE / Inhibitor / Phosphonamidate / Protease
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-JC2 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.249 Å
AuthorsCramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind Germany
CitationJournal: J. Med. Chem. / Year: 2017
Title: Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors.
Authors: Cramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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)35,39711
Polymers34,3601
Non-polymers1,03710
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-50 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.735, 92.735, 130.538
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-633-

HOH

21E-776-

HOH

31E-812-

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, 416 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-JC2 / (2~{S})-4-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]butanoic acid


Mass: 458.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H31N4O7P
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.9 M CsCl, 50 mM Tris (pH 7.5), 50% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2015
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.249→50 Å / Num. obs: 91757 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 1 / Rsym value: 0.066 / Net I/σ(I): 25.38
Reflection shellResolution: 1.249→1.32 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 4.94 / CC1/2: 0.938 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
Coot0.8 (revision 5201)model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8TLN

8tln


Resolution: 1.249→40.155 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 8.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1268 4588 5 %
Rwork0.1029 --
obs0.104 91748 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.249→40.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 56 406 2883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012624
X-RAY DIFFRACTIONf_angle_d1.153590
X-RAY DIFFRACTIONf_dihedral_angle_d19.866903
X-RAY DIFFRACTIONf_chiral_restr0.09379
X-RAY DIFFRACTIONf_plane_restr0.009477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2489-1.26310.14391470.12162801X-RAY DIFFRACTION98
1.2631-1.27790.14371510.11982865X-RAY DIFFRACTION100
1.2779-1.29350.13971510.11422876X-RAY DIFFRACTION100
1.2935-1.30990.13491500.11372849X-RAY DIFFRACTION100
1.3099-1.32710.15161520.1062882X-RAY DIFFRACTION100
1.3271-1.34530.13781500.10492857X-RAY DIFFRACTION100
1.3453-1.36450.1211510.10112865X-RAY DIFFRACTION100
1.3645-1.38490.12781510.09922874X-RAY DIFFRACTION100
1.3849-1.40650.15271510.09922867X-RAY DIFFRACTION100
1.4065-1.42960.13331510.09212871X-RAY DIFFRACTION100
1.4296-1.45420.10581520.09082878X-RAY DIFFRACTION100
1.4542-1.48070.12281510.08482878X-RAY DIFFRACTION100
1.4807-1.50920.11911510.08542864X-RAY DIFFRACTION100
1.5092-1.540.11851520.08222890X-RAY DIFFRACTION100
1.54-1.57350.10461530.07962898X-RAY DIFFRACTION100
1.5735-1.61010.10491510.07872868X-RAY DIFFRACTION100
1.6101-1.65030.08971520.07872901X-RAY DIFFRACTION100
1.6503-1.69490.11151520.08342885X-RAY DIFFRACTION100
1.6949-1.74480.13051530.08632899X-RAY DIFFRACTION100
1.7448-1.80110.12181520.08472895X-RAY DIFFRACTION100
1.8011-1.86550.10281530.09242911X-RAY DIFFRACTION100
1.8655-1.94020.11651540.09672914X-RAY DIFFRACTION100
1.9402-2.02850.11771530.09732923X-RAY DIFFRACTION100
2.0285-2.13540.11151550.09792928X-RAY DIFFRACTION100
2.1354-2.26920.11871540.10172930X-RAY DIFFRACTION100
2.2692-2.44440.10911550.10032950X-RAY DIFFRACTION100
2.4444-2.69040.13851560.10542957X-RAY DIFFRACTION100
2.6904-3.07950.14761570.10922992X-RAY DIFFRACTION100
3.0795-3.87940.141590.11793011X-RAY DIFFRACTION100
3.8794-40.17620.14361680.13063181X-RAY DIFFRACTION99

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