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- PDB-5dpe: Thermolysin in complex with inhibitor. -

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Basic information

Entry
Database: PDB / ID: 5dpe
TitleThermolysin in complex with inhibitor.
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-5H8 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsKrimmer, S.G. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC)268145-DrugProfilBind Germany
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2015
Title: Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data.
Authors: Krimmer, S.G. / Klebe, G.
History
DepositionSep 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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 / _struct_conn.ptnr2_label_asym_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)35,64614
Polymers34,3601
Non-polymers1,28613
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-46 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.690, 92.690, 130.261
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-757-

HOH

21E-794-

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 / Fragment: UNP residues 233-548 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 399 molecules

#2: Chemical ChemComp-5H8 / N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-3-methyl-L-valine / (6S,9S)-1-(benzyloxy)-9-(tert-butyl)-6-isobutyl-4-oxido-1,4,7-trioxo-2,5,8-triaza-4-phosphadecan-10-oate


Mass: 471.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34N3O7P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO, / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2012
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: 1.34→50 Å / Num. obs: 72715 / % possible obs: 97.6 % / Redundancy: 10.3 % / Rsym value: 0.063 / Net I/σ(I): 35.813
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 4.38 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1492refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8TLN

8tln


Resolution: 1.34→34.169 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1558 3649 5.03 %Random selection
Rwork0.1272 ---
obs0.1286 72495 97.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→34.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 71 386 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072590
X-RAY DIFFRACTIONf_angle_d1.1833537
X-RAY DIFFRACTIONf_dihedral_angle_d12.385898
X-RAY DIFFRACTIONf_chiral_restr0.073375
X-RAY DIFFRACTIONf_plane_restr0.006462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3402-1.35780.15471350.1372576X-RAY DIFFRACTION97
1.3578-1.37640.17681400.13812633X-RAY DIFFRACTION99
1.3764-1.39610.1841260.12752682X-RAY DIFFRACTION100
1.3961-1.41690.16831430.11912678X-RAY DIFFRACTION100
1.4169-1.43910.15481590.12332632X-RAY DIFFRACTION100
1.4391-1.46270.19481240.11972695X-RAY DIFFRACTION100
1.4627-1.48790.1811430.14452664X-RAY DIFFRACTION99
1.4879-1.5150.14851440.11572677X-RAY DIFFRACTION100
1.515-1.54410.16711380.10192687X-RAY DIFFRACTION100
1.5441-1.57560.13551670.09812648X-RAY DIFFRACTION100
1.5756-1.60990.13891660.09692664X-RAY DIFFRACTION100
1.6099-1.64730.12041620.09232671X-RAY DIFFRACTION100
1.6473-1.68850.14681240.09892720X-RAY DIFFRACTION100
1.6885-1.73420.11771570.09712661X-RAY DIFFRACTION100
1.7342-1.78520.13221490.09742708X-RAY DIFFRACTION100
1.7852-1.84280.11631580.09992690X-RAY DIFFRACTION100
1.8428-1.90870.15941200.1132134X-RAY DIFFRACTION80
1.9087-1.98510.21821400.18742481X-RAY DIFFRACTION91
1.9851-2.07540.11421240.10512738X-RAY DIFFRACTION100
2.0754-2.18480.12991480.10632714X-RAY DIFFRACTION100
2.1848-2.32170.22461030.19432079X-RAY DIFFRACTION75
2.3217-2.50090.15651330.11332746X-RAY DIFFRACTION100
2.5009-2.75250.13141370.122765X-RAY DIFFRACTION100
2.7525-3.15050.12871290.12372795X-RAY DIFFRACTION100
3.1505-3.96840.16651370.13392735X-RAY DIFFRACTION96
3.9684-34.18020.18171430.15192973X-RAY DIFFRACTION99

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