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- PDB-6x1m: Lon protease proteolytic domain complexed with covalent boronic a... -

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Basic information

Entry
Database: PDB / ID: 6x1m
TitleLon protease proteolytic domain complexed with covalent boronic acid inhibitor
ComponentsLon protease homolog, mitochondrial
KeywordsHYDROLASE / covalent inhibitor / proteolytic domain
Function / homology
Function and homology information


oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / response to aluminum ion / endopeptidase La / G-quadruplex DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins ...oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / response to aluminum ion / endopeptidase La / G-quadruplex DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid / insulin receptor substrate binding / Mitochondrial unfolded protein response (UPRmt) / chaperone-mediated protein complex assembly / DNA polymerase binding / response to hormone / Mitochondrial protein degradation / negative regulation of insulin receptor signaling pathway / proteolysis involved in protein catabolic process / mitochondrion organization / protein catabolic process / ADP binding / single-stranded DNA binding / cellular response to oxidative stress / sequence-specific DNA binding / response to hypoxia / single-stranded RNA binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Lon protease homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain ...Lon protease homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Ribosomal Protein S5; domain 2 - #10 / PUA-like superfamily / Ribosomal Protein S5; domain 2 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UKS / Lon protease homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsLee, C.C. / Spraggon, G.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Design of Selective LONP1 Inhibitors for Probing In Vitro Biology.
Authors: Kingsley, L.J. / He, X. / McNeill, M. / Nelson, J. / Nikulin, V. / Ma, Z. / Lu, W. / Zhou, V.W. / Manuia, M. / Kreusch, A. / Gao, M.Y. / Witmer, D. / Vaillancourt, M.T. / Lu, M. / ...Authors: Kingsley, L.J. / He, X. / McNeill, M. / Nelson, J. / Nikulin, V. / Ma, Z. / Lu, W. / Zhou, V.W. / Manuia, M. / Kreusch, A. / Gao, M.Y. / Witmer, D. / Vaillancourt, M.T. / Lu, M. / Greenblatt, S. / Lee, C. / Vashisht, A. / Bender, S. / Spraggon, G. / Michellys, P.Y. / Jia, Y. / Haling, J.R. / Lelais, G.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lon protease homolog, mitochondrial
B: Lon protease homolog, mitochondrial
C: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1615
Polymers71,3653
Non-polymers7972
Water00
1
A: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1862
Polymers23,7881
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lon protease homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1862
Polymers23,7881
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lon protease homolog, mitochondrial


Theoretical massNumber of molelcules
Total (without water)23,7881
Polymers23,7881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.769, 185.769, 159.773
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Lon protease homolog, mitochondrial / LONHs / Lon protease-like protein / LONP / Mitochondrial ATP-dependent protease Lon / Serine protease 15


Mass: 23788.221 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LONP1, PRSS15 / Production host: Escherichia coli (E. coli) / References: UniProt: P36776, endopeptidase La
#2: Chemical ChemComp-UKS / [(1R)-4-phenyl-1-{[N-(pyrazine-2-carbonyl)-D-norvalyl]amino}butyl]boronic acid


Mass: 398.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27BN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2% PEG 400; 2.0M (NH4)2SO4 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 16306 / % possible obs: 97.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.492 / Rpim(I) all: 0.207 / Rrim(I) all: 0.535 / Χ2: 0.965 / Net I/σ(I): 1.9 / Num. measured all: 104716
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.313.22.5366060.1471.332.8920.86672.7
3.31-3.373.52.1417000.1461.1342.4470.84787.4
3.37-3.434.12.1487940.1721.1112.4410.86593.6
3.43-3.54.91.7578030.3140.841.9590.88697.1
3.5-3.585.61.6837950.3260.7611.8540.91398.5
3.58-3.6661.3678290.4970.5961.4960.93399.3
3.66-3.756.50.978210.5910.4131.0570.94799.9
3.75-3.856.61.088470.6120.4491.1710.95100
3.85-3.976.91.0088290.7640.4151.0920.967100
3.97-4.097.10.8388230.7220.3390.9060.954100
4.09-4.247.10.6948380.8520.2790.7490.992100
4.24-4.417.20.4588380.9020.1830.4931.05100
4.41-4.617.30.4538250.9180.180.4881.047100
4.61-4.857.40.4258370.9420.1670.4571.026100
4.85-5.167.40.4338390.9290.1710.4661.046100
5.16-5.567.40.5438330.8790.2150.5840.996100
5.56-6.117.30.4648480.8970.1840.4990.974100
6.11-77.10.4038540.9220.1620.4350.969100
7-8.817.10.168550.990.0640.1720.949100
8.81-507.10.0678920.9980.0270.0720.864100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 6WYS

6wys


Resolution: 3.51→48.39 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3077 590 4.82 %
Rwork0.2112 11653 -
obs0.2158 12243 91.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 299.93 Å2 / Biso mean: 79.4339 Å2 / Biso min: 1.29 Å2
Refinement stepCycle: final / Resolution: 3.51→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 58 0 4339
Biso mean--58.95 --
Num. residues----577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.51-3.860.35581010.25812053215465
3.86-4.420.3171670.21531423309100
4.42-5.570.27531500.201531903340100
5.57-48.390.30881720.232683440100
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)
14.88941.21382.07014.67810.84047.0097-0.0059-0.23420.46230.1264-0.185-0.3223-0.3517-0.45790.14050.2744-0.0267-0.01290.53760.11850.322827.2845326.846560.8983
26.0148-0.2991-0.98453.24460.0881.15060.43620.65820.9317-0.2819-0.03080.35310.01320.0990.21330.87940.3102-0.0190.17310.00670.349317.3522336.901653.9931
31.0860.4505-2.22521.0936-0.51094.70910.1036-0.12040.08480.2380.1771-0.0296-0.11410.1537-0.5560.53020.1472-0.18220.53810.01130.55521.315328.587255.3545
41.29180.46122.5314.06570.48485.03010.20270.01140.1475-0.1048-0.0841-0.3626-0.31870.5099-0.20420.2817-0.07880.08260.38120.03270.585330.4918339.171362.962
57.25630.82-2.58378.51471.13243.5277-1.01170.241-0.31760.17540.2079-0.38320.20830.56530.42620.4392-0.08320.02560.46580.19610.533537.7273344.858268.499
66.1222-0.42041.05066.4745-6.10485.8341-0.2107-0.3826-0.2548-0.44950.1799-1.0573-1.6550.4954-0.00260.747-0.26160.08870.87680.13330.658434.2248343.348549.7436
72.9794-0.4298-0.02314.66582.33083.0683-0.574-0.2972-0.79770.63020.61390.06220.85390.1823-0.37760.42340.12960.19340.49380.05130.620622.6365295.856864.17
86.67080.01730.73533.2089-2.91915.2384-0.1078-0.058-0.132-0.2043-0.1346-0.23730.5881-0.13220.17730.4165-0.02550.14520.3843-0.09610.434117.3844309.133855.9974
94.25391.0774-2.45442.113-2.39084.3037-0.11230.08890.4766-0.51810.31340.3276-0.61430.0161-0.38690.5347-0.24680.05940.49090.07830.465915.6009306.473854.307
103.57910.7842.19941.5762-1.00646.66920.11910.3229-0.4150.02610.3074-0.13570.62831.1156-0.29860.43990.04810.18440.5799-0.01380.532732.3309303.496962.8825
110.6116-0.98320.71174.9884-2.89723.4486-0.2-0.2556-0.3607-0.02350.65560.06060.5734-0.5622-0.18970.4303-0.05260.24570.9097-0.04050.694343.6062319.397350.6244
124.6496-0.2399-0.79563.5874-0.64192.4839-0.1811-0.00910.7188-0.3560.6609-0.4835-1.1997-0.0017-0.41620.7919-0.11590.33310.5371-0.08850.724742.1527336.085739.1494
134.318-0.6012.20715.01752.77173.04490.00661.23390.5328-1.44270.615-0.0401-1.36160.024-0.10780.73540.00220.12190.85370.25780.534542.0854333.043425.9451
141.8323-0.21690.9543.93881.63051.29130.11450.2950.33550.19840.56320.0961-0.252-0.2918-0.41970.4356-0.06310.19950.66290.23590.602345.5108328.295235.5297
154.8165-1.05533.68312.20920.10463.32280.43090.5805-0.2126-0.03210.2388-0.1745-0.15830.5813-0.42950.4601-0.07760.15360.58620.02370.510753.3613316.5638.8206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 754 through 807 )A754 - 807
2X-RAY DIFFRACTION2chain 'A' and (resid 808 through 828 )A808 - 828
3X-RAY DIFFRACTION3chain 'A' and (resid 829 through 856 )A829 - 856
4X-RAY DIFFRACTION4chain 'A' and (resid 857 through 921 )A857 - 921
5X-RAY DIFFRACTION5chain 'A' and (resid 922 through 938 )A922 - 938
6X-RAY DIFFRACTION6chain 'A' and (resid 939 through 955 )A939 - 955
7X-RAY DIFFRACTION7chain 'B' and (resid 753 through 773 )B753 - 773
8X-RAY DIFFRACTION8chain 'B' and (resid 774 through 828 )B774 - 828
9X-RAY DIFFRACTION9chain 'B' and (resid 829 through 853 )B829 - 853
10X-RAY DIFFRACTION10chain 'B' and (resid 854 through 949 )B854 - 949
11X-RAY DIFFRACTION11chain 'C' and (resid 746 through 773 )C746 - 773
12X-RAY DIFFRACTION12chain 'C' and (resid 774 through 807 )C774 - 807
13X-RAY DIFFRACTION13chain 'C' and (resid 808 through 838 )C808 - 838
14X-RAY DIFFRACTION14chain 'C' and (resid 839 through 889 )C839 - 889
15X-RAY DIFFRACTION15chain 'C' and (resid 890 through 948 )C890 - 948

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