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

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Basic information

Entry
Database: PDB / ID: 6ymr
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
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-OZE / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionApr 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 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)35,2489
Polymers34,3601
Non-polymers8878
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-44 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.768, 92.768, 129.602
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-705-

HOH

21E-710-

HOH

31E-727-

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 , 5 types, 262 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.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-OZE / (((R)-1-(((benzyloxy)carbonyl)amino)-2-phenylethyl)oxidophosphoryl)glycyl-L-leucinate / (2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{R})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]ethanoylamino]p entanoic acid


Mass: 505.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N3O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 47.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M CsCl, 50 mM 3-Morpholinopropane-1-sulfonic acid, 50% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→43.67 Å / Num. obs: 43405 / % possible obs: 98.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.05 Å2 / Rrim(I) all: 0.114 / Rsym value: 0.105 / Net I/σ(I): 10.63
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.83 % / Mean I/σ(I) obs: 2.67 / Num. unique obs: 6830 / CC1/2: 0.88 / Rrim(I) all: 0.546 / Rsym value: 0.506

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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: 1.6→43.67 Å / SU ML: 0.1348 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.3846
RfactorNum. reflection% reflection
Rfree0.1781 2171 5 %
Rwork0.1351 --
obs0.1373 43404 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 48 254 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742585
X-RAY DIFFRACTIONf_angle_d0.91683533
X-RAY DIFFRACTIONf_chiral_restr0.0561375
X-RAY DIFFRACTIONf_plane_restr0.006481
X-RAY DIFFRACTIONf_dihedral_angle_d13.38981482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.2161310.13112488X-RAY DIFFRACTION97.83
1.63-1.670.20581330.1282523X-RAY DIFFRACTION98.15
1.67-1.710.2131330.12752530X-RAY DIFFRACTION97.94
1.71-1.760.19971320.12432507X-RAY DIFFRACTION98.54
1.76-1.810.17451350.11882555X-RAY DIFFRACTION98.61
1.81-1.870.19311330.12112532X-RAY DIFFRACTION98.74
1.87-1.940.18951290.11712456X-RAY DIFFRACTION95.11
1.94-2.020.15781360.10882574X-RAY DIFFRACTION99.12
2.02-2.110.17561340.10462559X-RAY DIFFRACTION99.12
2.11-2.220.14991360.10842585X-RAY DIFFRACTION99.27
2.22-2.360.1621370.11082585X-RAY DIFFRACTION99.23
2.36-2.540.13981370.11582607X-RAY DIFFRACTION99.56
2.54-2.790.17021350.12572574X-RAY DIFFRACTION97.38
2.79-3.20.141400.13042651X-RAY DIFFRACTION99.86
3.2-4.030.1731420.14632701X-RAY DIFFRACTION99.96
4.03-43.670.23311480.18682806X-RAY DIFFRACTION98.01

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