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- PDB-5n3y: Thermolysin in complex with inhibitor JC267 -

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Basic information

Entry
Database: PDB / ID: 5n3y
TitleThermolysin in complex with inhibitor JC267
ComponentsThermolysin
KeywordsHYDROLASE / Inhibitor / Phosphonamidate / 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-8L2 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.339 Å
AuthorsCramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors.
Authors: Cramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G.
History
DepositionFeb 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,46112
Polymers34,3601
Non-polymers1,10111
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-47 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.681, 92.681, 130.671
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-761-

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 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 383 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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-8L2 / (2~{S})-3-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]propanoic acid


Mass: 444.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N4O7P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4 mM TLN, 1.9 M CsCl, 50% DMSO, 50 mM Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.339→50 Å / Num. obs: 74695 / % possible obs: 99.9 % / Redundancy: 9.61 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.07 / Net I/σ(I): 22.62
Reflection shellResolution: 1.339→1.419 Å / Redundancy: 9.79 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.79 / Num. unique obs: 11813 / CC1/2: 0.94 / Rrim(I) all: 0.51 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8TLN

8tln


Resolution: 1.339→40.132 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 9.52
RfactorNum. reflection% reflection
Rfree0.1382 3735 5 %
Rwork0.1103 --
obs0.1117 74691 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.339→40.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 59 372 2847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112578
X-RAY DIFFRACTIONf_angle_d1.1613521
X-RAY DIFFRACTIONf_dihedral_angle_d15.324876
X-RAY DIFFRACTIONf_chiral_restr0.09374
X-RAY DIFFRACTIONf_plane_restr0.009464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.339-1.3560.18711310.12992496X-RAY DIFFRACTION97
1.356-1.37380.15991360.11932586X-RAY DIFFRACTION100
1.3738-1.39260.15181370.11382597X-RAY DIFFRACTION100
1.3926-1.41250.12751350.10722575X-RAY DIFFRACTION100
1.4125-1.43360.15921380.09912604X-RAY DIFFRACTION100
1.4336-1.4560.1481350.09842580X-RAY DIFFRACTION100
1.456-1.47990.12671370.09222600X-RAY DIFFRACTION100
1.4799-1.50540.14421360.09152584X-RAY DIFFRACTION100
1.5054-1.53280.12521370.08722607X-RAY DIFFRACTION100
1.5328-1.56230.12861370.08482591X-RAY DIFFRACTION100
1.5623-1.59420.13071370.08422609X-RAY DIFFRACTION100
1.5942-1.62880.12331370.08252596X-RAY DIFFRACTION100
1.6288-1.66670.11471370.08322613X-RAY DIFFRACTION100
1.6667-1.70840.12621370.08532600X-RAY DIFFRACTION100
1.7084-1.75460.12511380.08532619X-RAY DIFFRACTION100
1.7546-1.80620.11391370.08582614X-RAY DIFFRACTION100
1.8062-1.86450.11991390.09492625X-RAY DIFFRACTION100
1.8645-1.93120.12041380.09872629X-RAY DIFFRACTION100
1.9312-2.00850.12291380.10462629X-RAY DIFFRACTION100
2.0085-2.09990.14411390.10772630X-RAY DIFFRACTION100
2.0999-2.21060.14581390.10422641X-RAY DIFFRACTION100
2.2106-2.34910.13141390.10792637X-RAY DIFFRACTION100
2.3491-2.53040.13871400.112671X-RAY DIFFRACTION100
2.5304-2.7850.12161410.11252678X-RAY DIFFRACTION100
2.785-3.18790.13671430.12312709X-RAY DIFFRACTION100
3.1879-4.01580.16331440.13182739X-RAY DIFFRACTION100
4.0158-40.15010.1531530.14132897X-RAY DIFFRACTION99

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