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- PDB-5n31: Thermolysin in complex with inhibitor JC277 -

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Basic information

Entry
Database: PDB / ID: 5n31
TitleThermolysin in complex with inhibitor JC277
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-8LB / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.368 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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)35,42511
Polymers34,3601
Non-polymers1,06510
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-50 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.796, 92.796, 130.876
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-770-

HOH

21E-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, 411 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-8LB / (2~{S})-6-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]hexanoic acid


Mass: 486.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H35N4O7P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
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: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.368→50 Å / Num. obs: 70390 / % possible obs: 99.8 % / Redundancy: 9.6 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.07 / Net I/σ(I): 22.98
Reflection shellResolution: 1.368→1.449 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.59 / Num. unique obs: 11100 / CC1/2: 0.93 / Rrim(I) all: 0.5 / % possible all: 99.1

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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: 1.368→26.739 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 9.73
RfactorNum. reflection% reflection
Rfree0.1336 3519 5 %
Rwork0.107 --
obs0.1083 70383 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.368→26.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 57 401 2870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092596
X-RAY DIFFRACTIONf_angle_d1.073550
X-RAY DIFFRACTIONf_dihedral_angle_d18.182887
X-RAY DIFFRACTIONf_chiral_restr0.084377
X-RAY DIFFRACTIONf_plane_restr0.007469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3681-1.38690.21911330.14412531X-RAY DIFFRACTION96
1.3869-1.40670.18281390.12452641X-RAY DIFFRACTION100
1.4067-1.42770.14511380.10672621X-RAY DIFFRACTION100
1.4277-1.450.17731390.09842642X-RAY DIFFRACTION100
1.45-1.47370.14611390.09232629X-RAY DIFFRACTION100
1.4737-1.49920.11411390.08862644X-RAY DIFFRACTION100
1.4992-1.52640.13891390.08932644X-RAY DIFFRACTION100
1.5264-1.55580.13911390.08572633X-RAY DIFFRACTION100
1.5558-1.58750.13381380.08682633X-RAY DIFFRACTION100
1.5875-1.6220.13851400.08262660X-RAY DIFFRACTION100
1.622-1.65980.12191400.08242659X-RAY DIFFRACTION100
1.6598-1.70130.1151380.08692627X-RAY DIFFRACTION100
1.7013-1.74730.11311410.08652672X-RAY DIFFRACTION100
1.7473-1.79870.12071390.08852640X-RAY DIFFRACTION100
1.7987-1.85670.11431410.09292677X-RAY DIFFRACTION100
1.8567-1.9230.13431400.09942658X-RAY DIFFRACTION100
1.923-20.13931400.10192663X-RAY DIFFRACTION100
2-2.0910.13941410.10642688X-RAY DIFFRACTION100
2.091-2.20120.12751420.10152700X-RAY DIFFRACTION100
2.2012-2.3390.13191410.1032680X-RAY DIFFRACTION100
2.339-2.51950.1451430.10512711X-RAY DIFFRACTION100
2.5195-2.77280.11241440.10512724X-RAY DIFFRACTION100
2.7728-3.17350.13041430.11192735X-RAY DIFFRACTION100
3.1735-3.99610.13771480.12372795X-RAY DIFFRACTION100
3.9961-26.74430.13481550.13442957X-RAY DIFFRACTION100

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