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- PDB-6y4i: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors o... -

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Basic information

Entry
Database: PDB / ID: 6y4i
TitleStructural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
ComponentsThermolysin
KeywordsHYDROLASE / Phosphoramidate Inhibitor / Protease
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
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 ...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 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Chem-0PK / : / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsKljajic, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
Authors: Kljajic, M. / Gerber, H.-D. / Heine, A. / Klebe, G.
History
DepositionFeb 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,55112
Polymers34,3601
Non-polymers1,19111
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-72 kcal/mol
Surface area12350 Å2
Unit cell
Length a, b, c (Å)92.612, 92.612, 129.969
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11E-768-

HOH

21E-798-

HOH

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Thermolysin / Neutral protease


Mass: 34360.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: nprS, nprM / Production host: Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, thermolysin

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Non-polymers , 6 types, 373 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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-0PK / N-[(S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}-2-phenylethyl](hydroxy)phosphoryl]-L-leucyl-L-alanine / ZFPLA


Type: peptide-like / Mass: 519.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H34N3O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 47.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M CsCl, 50 mM Tris(hydroxymethyl)aminomethan, 50% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.16→46.31 Å / Num. obs: 113185 / % possible obs: 99.7 % / Redundancy: 6.42 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.099 / Rsym value: 0.091 / Net I/σ(I): 10.36
Reflection shellResolution: 1.16→1.23 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 17875 / CC1/2: 0.879 / Rrim(I) all: 0.525 / Rsym value: 0.482 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LVD

5lvd


Resolution: 1.16→46.31 Å / SU ML: 0.0798 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.4409
RfactorNum. reflection% reflection
Rfree0.1396 5660 5 %
Rwork0.1263 --
obs0.127 113182 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.78 Å2
Refinement stepCycle: LAST / Resolution: 1.16→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 58 362 2836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582611
X-RAY DIFFRACTIONf_angle_d0.93253569
X-RAY DIFFRACTIONf_chiral_restr0.0793380
X-RAY DIFFRACTIONf_plane_restr0.006483
X-RAY DIFFRACTIONf_dihedral_angle_d16.4694916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.170.23241800.19253422X-RAY DIFFRACTION96.98
1.17-1.190.1841840.17273483X-RAY DIFFRACTION98.97
1.19-1.20.17431870.15823549X-RAY DIFFRACTION99.41
1.2-1.220.16911850.15763519X-RAY DIFFRACTION99.46
1.22-1.230.15541850.15213517X-RAY DIFFRACTION99.7
1.23-1.250.18311860.14453535X-RAY DIFFRACTION99.57
1.25-1.270.17431860.14023542X-RAY DIFFRACTION99.71
1.27-1.290.16181870.14193552X-RAY DIFFRACTION99.68
1.29-1.310.1531860.13573518X-RAY DIFFRACTION99.81
1.31-1.330.15491870.1293559X-RAY DIFFRACTION99.84
1.33-1.350.14921850.1223524X-RAY DIFFRACTION99.95
1.35-1.380.15291880.11533571X-RAY DIFFRACTION99.89
1.38-1.40.14411880.11973568X-RAY DIFFRACTION99.92
1.4-1.430.15181870.11593558X-RAY DIFFRACTION100
1.43-1.460.12171880.11473557X-RAY DIFFRACTION99.95
1.46-1.50.12821880.10813572X-RAY DIFFRACTION99.89
1.5-1.530.12221870.10723557X-RAY DIFFRACTION99.81
1.53-1.570.1261880.10113578X-RAY DIFFRACTION99.97
1.57-1.620.12111880.10383579X-RAY DIFFRACTION99.97
1.62-1.670.10771890.10463577X-RAY DIFFRACTION100
1.67-1.730.12811890.10663593X-RAY DIFFRACTION100
1.73-1.80.12111890.1063599X-RAY DIFFRACTION99.97
1.8-1.880.12831910.10863618X-RAY DIFFRACTION99.9
1.88-1.980.12481890.11143606X-RAY DIFFRACTION99.97
1.98-2.110.11911910.10783620X-RAY DIFFRACTION100
2.11-2.270.12861920.10883640X-RAY DIFFRACTION99.97
2.27-2.50.11681920.1133659X-RAY DIFFRACTION99.97
2.5-2.860.14181940.123673X-RAY DIFFRACTION99.56
2.86-3.60.13751960.1343729X-RAY DIFFRACTION99.95
3.6-46.310.16552080.16383948X-RAY DIFFRACTION99.71

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