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- PDB-4n5p: Thermolysin in complex with UBTLN20 -

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Basic information

Entry
Database: PDB / ID: 4n5p
TitleThermolysin in complex with UBTLN20
ComponentsThermolysin
Keywordshydrolase/hydrolase inhibitor / Protease / Metalloprotease / Hydrolysis of peptide bonds / 2-Phosphoramidon / 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 ...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
N~2~-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(3-METHYLBUTYL)-L-LEUCINAMIDE / Chem-2H0 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKrimmer, S.G. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2014
Title: Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors.
Authors: Krimmer, S.G. / Betz, M. / Heine, A. / Klebe, G.
History
DepositionOct 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Sep 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,51013
Polymers34,3601
Non-polymers1,15012
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.491, 92.491, 130.891
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-1044-

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, 485 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-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-2H0 / P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-1-(isopentylamino)-4-methyl-1-oxopentan-2-yl)phosphonamidic acid / N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(3-methylbutyl)-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 427.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34N3O5P
References: N~2~-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(3-METHYLBUTYL)-L-LEUCINAMIDE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
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 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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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 19, 2012 / Details: Mirror
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: 1.25→50 Å / Num. obs: 90096 / % possible obs: 98.5 % / Redundancy: 12.7 % / Biso Wilson estimate: 9.267 Å2 / Rsym value: 0.055 / Net I/σ(I): 42.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 3866 / Rsym value: 0.273 / % possible all: 86.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1492)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 8TLN

8tln


Resolution: 1.25→34.161 Å / SU ML: 0.08 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 10.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.134 4529 5.03 %random
Rwork0.1132 ---
obs0.1143 90046 98.53 %-
all-90096 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→34.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 62 473 2967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062693
X-RAY DIFFRACTIONf_angle_d1.1173680
X-RAY DIFFRACTIONf_dihedral_angle_d13.864963
X-RAY DIFFRACTIONf_chiral_restr0.079384
X-RAY DIFFRACTIONf_plane_restr0.005489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.16681450.12922379X-RAY DIFFRACTION85
1.2642-1.27910.15071140.12482557X-RAY DIFFRACTION89
1.2791-1.29460.13741390.11452604X-RAY DIFFRACTION92
1.2946-1.3110.14091510.11442714X-RAY DIFFRACTION95
1.311-1.32830.12671560.10932777X-RAY DIFFRACTION98
1.3283-1.34650.16091290.11142832X-RAY DIFFRACTION99
1.3465-1.36570.13191500.11052825X-RAY DIFFRACTION100
1.3657-1.38610.12751440.10632853X-RAY DIFFRACTION100
1.3861-1.40780.12951380.09862902X-RAY DIFFRACTION100
1.4078-1.43080.13561480.0972854X-RAY DIFFRACTION100
1.4308-1.45550.12471720.09552832X-RAY DIFFRACTION100
1.4555-1.4820.12681640.0942849X-RAY DIFFRACTION100
1.482-1.51050.12351370.09592873X-RAY DIFFRACTION100
1.5105-1.54130.11341590.09392897X-RAY DIFFRACTION100
1.5413-1.57480.13341450.09462827X-RAY DIFFRACTION100
1.5748-1.61150.141780.0972835X-RAY DIFFRACTION100
1.6115-1.65180.11561330.09822954X-RAY DIFFRACTION100
1.6518-1.69640.12841360.09892840X-RAY DIFFRACTION100
1.6964-1.74630.12291540.10232916X-RAY DIFFRACTION100
1.7463-1.80270.1241400.12882X-RAY DIFFRACTION100
1.8027-1.86710.12111430.10452891X-RAY DIFFRACTION100
1.8671-1.94190.10881850.10892859X-RAY DIFFRACTION100
1.9419-2.03030.13391670.11062898X-RAY DIFFRACTION100
2.0303-2.13730.11351430.10842935X-RAY DIFFRACTION100
2.1373-2.27120.12881610.11092898X-RAY DIFFRACTION100
2.2712-2.44650.14321720.1192914X-RAY DIFFRACTION100
2.4465-2.69260.13861470.1242966X-RAY DIFFRACTION100
2.6926-3.0820.14121420.12292999X-RAY DIFFRACTION100
3.082-3.88210.13721670.11953006X-RAY DIFFRACTION100
3.8821-34.17360.16081700.13583149X-RAY DIFFRACTION99

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