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- PDB-5n2x: Thermolysin in complex with inhibitor JC272 -

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Basic information

Entry
Database: PDB / ID: 5n2x
TitleThermolysin in complex with inhibitor JC272
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-8KN / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.209 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

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,41111
Polymers34,3601
Non-polymers1,05110
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-48 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.751, 92.751, 130.348
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-756-

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, 367 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-8KN / (2~{S})-5-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]pentanoic acid


Mass: 472.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H33N4O7P
#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.: 357 / 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: 47.78 %
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: 1.209→50 Å / Num. obs: 100719 / % possible obs: 99.8 % / Redundancy: 11.8 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.07 / Net I/σ(I): 23.89
Reflection shellResolution: 1.209→1.28 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.68 / Num. unique obs: 15957 / CC1/2: 0.94 / Rrim(I) all: 0.51 / % possible all: 99.3

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Processing

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

8tln


Resolution: 1.209→40.162 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 9.03
RfactorNum. reflection% reflection
Rfree0.1272 5036 5 %
Rwork0.1106 --
obs0.1114 100710 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.209→40.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 57 357 2830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072597
X-RAY DIFFRACTIONf_angle_d1.0233552
X-RAY DIFFRACTIONf_dihedral_angle_d18.059887
X-RAY DIFFRACTIONf_chiral_restr0.082378
X-RAY DIFFRACTIONf_plane_restr0.007469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2095-1.22320.16951620.13883092X-RAY DIFFRACTION98
1.2232-1.23760.13561650.12383136X-RAY DIFFRACTION100
1.2376-1.25270.14341660.12093139X-RAY DIFFRACTION100
1.2527-1.26860.13071650.11733136X-RAY DIFFRACTION100
1.2686-1.28520.15481650.11623134X-RAY DIFFRACTION100
1.2852-1.30290.14711640.11283118X-RAY DIFFRACTION100
1.3029-1.32150.13231650.10823144X-RAY DIFFRACTION100
1.3215-1.34120.12841660.10613149X-RAY DIFFRACTION100
1.3412-1.36220.12781660.10033156X-RAY DIFFRACTION100
1.3622-1.38450.14051660.10033159X-RAY DIFFRACTION100
1.3845-1.40840.13231660.09933149X-RAY DIFFRACTION100
1.4084-1.4340.1171660.09243147X-RAY DIFFRACTION100
1.434-1.46160.12711660.0913167X-RAY DIFFRACTION100
1.4616-1.49140.11321660.08863157X-RAY DIFFRACTION100
1.4914-1.52380.11571680.08633182X-RAY DIFFRACTION100
1.5238-1.55930.10331660.08473146X-RAY DIFFRACTION100
1.5593-1.59830.10471680.0863198X-RAY DIFFRACTION100
1.5983-1.64150.10751660.08693156X-RAY DIFFRACTION100
1.6415-1.68980.10441680.09093197X-RAY DIFFRACTION100
1.6898-1.74430.10621670.09133175X-RAY DIFFRACTION100
1.7443-1.80670.10761680.09083186X-RAY DIFFRACTION100
1.8067-1.8790.11221690.10043205X-RAY DIFFRACTION100
1.879-1.96450.12041680.10513196X-RAY DIFFRACTION100
1.9645-2.06810.11981690.10733217X-RAY DIFFRACTION100
2.0681-2.19760.11931700.10833232X-RAY DIFFRACTION100
2.1976-2.36730.11811700.1093223X-RAY DIFFRACTION100
2.3673-2.60550.14011710.11333258X-RAY DIFFRACTION100
2.6055-2.98240.14551730.11653284X-RAY DIFFRACTION100
2.9824-3.75710.1461750.12943324X-RAY DIFFRACTION100
3.7571-40.18450.13061860.13793512X-RAY DIFFRACTION100

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