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- PDB-5ma7: Structure of thermolysin in complex with inhibitor (JC306). -

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Basic information

Entry
Database: PDB / ID: 5ma7
TitleStructure of thermolysin in complex with inhibitor (JC306).
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-7K0 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKrimmer, S.G. / Cramer, J. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind Germany
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin.
Authors: Krimmer, S.G. / Cramer, J. / Schiebel, J. / Heine, A. / Klebe, G.
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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 / 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

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,52713
Polymers34,3601
Non-polymers1,16712
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-47 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.754, 92.754, 129.766
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

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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, 392 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-7K0 / (2~{S})-2-[[(2~{S})-3-azanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]-4-methyl-pentanoic acid


Mass: 444.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N4O7P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO DOUBLE CRYSTAL MONOCHROMATOR

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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: Aug 26, 2016
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: 1.3→50 Å / Num. obs: 80990 / % possible obs: 99.8 % / Redundancy: 9.48 % / Rsym value: 0.053 / Net I/σ(I): 26.11
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 8.68 % / Mean I/σ(I) obs: 4.38 / Num. unique all: 12879 / Rsym value: 0.49 / % possible all: 99.6

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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: 1.3→43.672 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 10.9
RfactorNum. reflection% reflection
Rfree0.1389 4050 5 %
Rwork0.1121 --
obs0.1134 80989 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→43.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 63 380 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012615
X-RAY DIFFRACTIONf_angle_d1.1673573
X-RAY DIFFRACTIONf_dihedral_angle_d18.135894
X-RAY DIFFRACTIONf_chiral_restr0.093379
X-RAY DIFFRACTIONf_plane_restr0.008471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3003-1.31560.19531360.17232592X-RAY DIFFRACTION99
1.3156-1.33160.18571380.15052616X-RAY DIFFRACTION100
1.3316-1.34850.1791380.142616X-RAY DIFFRACTION100
1.3485-1.36620.19261370.14222610X-RAY DIFFRACTION100
1.3662-1.38490.16241370.132605X-RAY DIFFRACTION99
1.3849-1.40470.16091370.12062605X-RAY DIFFRACTION100
1.4047-1.42570.1511380.11342619X-RAY DIFFRACTION100
1.4257-1.4480.1561380.11062613X-RAY DIFFRACTION100
1.448-1.47170.13391380.10572630X-RAY DIFFRACTION100
1.4717-1.49710.14751390.10252628X-RAY DIFFRACTION100
1.4971-1.52430.14591370.09732616X-RAY DIFFRACTION100
1.5243-1.55360.1231380.09392622X-RAY DIFFRACTION100
1.5536-1.58530.14111390.08952626X-RAY DIFFRACTION100
1.5853-1.61980.13141380.08982624X-RAY DIFFRACTION100
1.6198-1.65750.13671390.08982656X-RAY DIFFRACTION100
1.6575-1.6990.13141380.09242623X-RAY DIFFRACTION100
1.699-1.74490.12641390.09052642X-RAY DIFFRACTION100
1.7449-1.79620.14471390.08812637X-RAY DIFFRACTION100
1.7962-1.85420.13511400.09492657X-RAY DIFFRACTION100
1.8542-1.92050.10641390.09242647X-RAY DIFFRACTION100
1.9205-1.99740.12791400.09612652X-RAY DIFFRACTION100
1.9974-2.08830.12431410.0992671X-RAY DIFFRACTION100
2.0883-2.19840.1011400.09492677X-RAY DIFFRACTION100
2.1984-2.33610.10571410.09652676X-RAY DIFFRACTION100
2.3361-2.51650.12421410.10712681X-RAY DIFFRACTION100
2.5165-2.76970.1341430.10742704X-RAY DIFFRACTION100
2.7697-3.17030.14361430.11832728X-RAY DIFFRACTION100
3.1703-3.99390.14441450.12662756X-RAY DIFFRACTION99
3.9939-43.69640.17031540.15012910X-RAY DIFFRACTION99

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