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- PDB-4h57: Thermolysin inhibition -

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Basic information

Entry
Database: PDB / ID: 4h57
TitleThermolysin inhibition
ComponentsThermolysin
KeywordsHYDROLASE/HYDROLASE inhibitor / PROTEASE PHOSPHONAMIDATE INHIBITOR / METAL-BINDING / METALLOPROTEASE / PROTEASE / SECRETED / HYDROLASE-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 / Thermolysin metallopeptidase, alpha-helical 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
CBZ-GLY-P-LEU-LEU (ZGPLL) / Chem-0PJ / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsEnglert, L. / Biela, A. / Heine, A. / Klebe, G.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Dissecting the hydrophobic effect on the molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin.
Authors: Biela, A. / Nasief, N.N. / Betz, M. / Heine, A. / Hangauer, D. / Klebe, G.
#1: Journal: Biochim.Biophys.Acta / Year: 2010
Title: Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: Binding of phosphonamidate to the S1'-pocket of thermolysin
Authors: Englert, L. / Biela, A. / Zayed, M. / Heine, A. / Hangauer, D. / Klebe, G.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 3, 2012ID: 3FWD
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Other
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: 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 / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,64614
Polymers34,3601
Non-polymers1,28613
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.452, 92.452, 129.778
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
11A-650-

HOH

21A-738-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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, 341 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-0PJ / N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-leucine / ZGPLL


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 471.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34N3O7P / References: CBZ-GLY-P-LEU-LEU (ZGPLL)
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 47.21 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50MM TRIS/HCL, 50%DMSO, 1.9M CSCL,, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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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: Jun 20, 2008 / Details: DOUBLE CRYSTAL MONOCHROMATOR
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: 1.56→27 Å / Num. all: 46395 / Num. obs: 46395 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.075 / Net I/σ(I): 15.4
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.357 / % possible all: 87.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1TMN

1tmn


Resolution: 1.56→22.632 Å / SU ML: 0.12 / Cross valid method: Free R / σ(F): 1.34 / Phase error: 14.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 2317 5 %RANDOM
Rwork0.1478 ---
obs0.1488 46352 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→22.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 71 328 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122643
X-RAY DIFFRACTIONf_angle_d1.0783742
X-RAY DIFFRACTIONf_dihedral_angle_d12.787917
X-RAY DIFFRACTIONf_chiral_restr0.077378
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5595-1.59130.23291180.20692296X-RAY DIFFRACTION88
1.5913-1.62590.20631320.17282407X-RAY DIFFRACTION93
1.6259-1.66370.18281250.16492508X-RAY DIFFRACTION97
1.6637-1.70530.20871260.16182564X-RAY DIFFRACTION99
1.7053-1.75140.20491480.15442596X-RAY DIFFRACTION100
1.7514-1.80290.1821340.14272577X-RAY DIFFRACTION100
1.8029-1.86110.16141360.13792616X-RAY DIFFRACTION100
1.8611-1.92760.17361330.14762599X-RAY DIFFRACTION100
1.9276-2.00470.16111260.13892623X-RAY DIFFRACTION100
2.0047-2.09590.15361490.13692590X-RAY DIFFRACTION100
2.0959-2.20630.15021210.1292636X-RAY DIFFRACTION100
2.2063-2.34440.17071350.13692625X-RAY DIFFRACTION99
2.3444-2.52520.16091420.13842615X-RAY DIFFRACTION99
2.5252-2.77890.15751520.142636X-RAY DIFFRACTION99
2.7789-3.18010.14241310.14382674X-RAY DIFFRACTION99
3.1801-4.00290.16911580.142675X-RAY DIFFRACTION99
4.0029-22.63440.16921510.17032798X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.692.0328-0.20662.7643-1.02411.2537-0.00020.1221-0.0339-0.21210.0031-0.00810.00130.0206-0.0290.1245-0.01610.0080.1463-0.02640.0713-27.849427.1109-10.9629
20.805-0.02460.30140.66360.0930.2503-0.00140.0241-0.025-0.0499-0.0145-0.00150.0067-0.02770.01460.0882-0.02180.02860.1128-0.00880.0693-24.208331.9359-1.3383
30.5525-0.21320.2660.5814-0.08860.53280.00170.08390.0404-0.0457-0.0339-0.1015-0.01740.10280.02680.0771-0.02210.03560.1240.0050.1197-7.129233.57551.3204
46.1636-2.45370.88382.3027-0.3061.5422-0.148-0.11130.3060.14840.0128-0.3074-0.1190.13510.09550.1306-0.0435-0.01630.15340.00850.18642.768741.245812.4176
51.8478-0.4744-0.40260.44990.19130.5662-0.02190.1008-0.088-0.01860.0055-0.10890.03370.15550.01220.1010.0040.02790.19210.0180.15487.788926.31045.8801
62.1238-0.9047-1.22083.36872.44514.3724-0.0033-0.0285-0.23970.1164-0.0849-0.02980.2533-0.05830.10150.0923-0.00310.01490.10220.0320.1592-5.439520.643112.9116
71.95660.5228-0.39575.64840.84711.861-0.0804-0.2308-0.36540.367-0.0151-0.09340.24680.09560.10450.15150.02210.02330.18950.05720.19140.963820.312417.8142
82.13510.3514-0.20077.21090.91661.8313-0.0664-0.1931-0.39850.0677-0.0164-0.47220.22280.2410.06790.1330.05010.02620.20570.05570.23258.417819.157512.9882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 211 )
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 232 )
5X-RAY DIFFRACTION5chain 'A' and (resid 233 through 259 )
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 296 )
8X-RAY DIFFRACTION8chain 'A' and (resid 297 through 316 )

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