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- PDB-5n2t: Thermolysin in complex with inhibitor JC287 -

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Basic information

Entry
Database: PDB / ID: 5n2t
TitleThermolysin in complex with inhibitor JC287
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-8KK / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.379 Å
AuthorsCramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G.
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
DepositionFeb 8, 2017Deposition 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: 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

Downloads & links

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,31311
Polymers34,3601
Non-polymers95310
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-41 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.047, 93.047, 130.795
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-767-

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 , 5 types, 378 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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-8KK / ~{N}-[(2~{S})-1-(3-azanylpropylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid


Mass: 414.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H31N4O5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4 mM TLN, 1.9 M CsCl, 50% DMSO, 50 mM Tris-HCl, pH 7.5

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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 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.379→50 Å / Num. obs: 69141 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 28.36
Reflection shellResolution: 1.379→1.459 Å / Redundancy: 12 % / Rmerge(I) obs: 0.49 / Num. unique obs: 10972 / CC1/2: 0.942 / Rsym value: 0.51 / % possible all: 99.8

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Processing

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

8tln


Resolution: 1.379→46.523 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1384 3457 5 %
Rwork0.1124 --
obs0.1137 69136 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.379→46.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 49 368 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072585
X-RAY DIFFRACTIONf_angle_d0.9683531
X-RAY DIFFRACTIONf_dihedral_angle_d18.836886
X-RAY DIFFRACTIONf_chiral_restr0.08373
X-RAY DIFFRACTIONf_plane_restr0.007468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3792-1.39810.17191340.13162556X-RAY DIFFRACTION99
1.3981-1.41810.16511360.12242577X-RAY DIFFRACTION100
1.4181-1.43930.15151370.11782600X-RAY DIFFRACTION100
1.4393-1.46180.14271360.11032588X-RAY DIFFRACTION100
1.4618-1.48570.15241350.1022580X-RAY DIFFRACTION100
1.4857-1.51140.16161360.10112579X-RAY DIFFRACTION100
1.5114-1.53880.14121370.09882599X-RAY DIFFRACTION100
1.5388-1.56840.13271360.09392589X-RAY DIFFRACTION100
1.5684-1.60050.12051370.09252595X-RAY DIFFRACTION100
1.6005-1.63530.1241370.08682597X-RAY DIFFRACTION100
1.6353-1.67330.13771360.08962594X-RAY DIFFRACTION100
1.6733-1.71510.12851370.09182605X-RAY DIFFRACTION100
1.7151-1.76150.11071370.09132607X-RAY DIFFRACTION100
1.7615-1.81340.10991370.09052604X-RAY DIFFRACTION100
1.8134-1.87190.12661380.10072605X-RAY DIFFRACTION100
1.8719-1.93880.13631380.10262640X-RAY DIFFRACTION100
1.9388-2.01640.13721380.10712616X-RAY DIFFRACTION100
2.0164-2.10820.14861380.10762623X-RAY DIFFRACTION100
2.1082-2.21930.12431390.10442633X-RAY DIFFRACTION100
2.2193-2.35840.11581390.10522636X-RAY DIFFRACTION100
2.3584-2.54050.14271390.10712653X-RAY DIFFRACTION100
2.5405-2.79610.14471410.11132674X-RAY DIFFRACTION100
2.7961-3.20060.13931420.12062705X-RAY DIFFRACTION100
3.2006-4.03210.14061440.13122729X-RAY DIFFRACTION100
4.0321-46.550.15541530.13832895X-RAY DIFFRACTION100

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