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- PDB-6bg5: Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperi... -

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Basic information

Entry
Database: PDB / ID: 6bg5
TitleStructure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluoromethyl)phenyl)urea bound to DCN1
ComponentsEndolysin, DCN1-like protein 1 chimera
KeywordsHYDROLASE / LIGASE/INHIBITOR / E3 Ligase / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process ...positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / Neddylation / host cell cytoplasm / defense response to bacterium / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Lysozyme - #40 / Endolysin T4 type ...Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Recoverin; domain 1 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DQD / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGuy, R.K. / Schulman, B.A. / Scott, D.C. / Hammill, J.T.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation.
Authors: Hammill, J.T. / Scott, D.C. / Min, J. / Connelly, M.C. / Holbrook, G. / Zhu, F. / Matheny, A. / Yang, L. / Singh, B. / Schulman, B.A. / Guy, R.K.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin, DCN1-like protein 1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7712
Polymers44,3071
Non-polymers4631
Water12,466692
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.944, 96.763, 59.279
Angle α, β, γ (deg.)90.000, 105.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endolysin, DCN1-like protein 1 chimera / DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / ...DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / Squamous cell carcinoma-related oncogene / Lysis protein / Lysozyme / Muramidase


Mass: 44307.352 Da / Num. of mol.: 1 / Fragment: PONY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: E, DCUN1D1, DCUN1L1, RP42, SCCRO / Plasmid: pRSF DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, UniProt: Q96GG9, lysozyme
#2: Chemical ChemComp-DQD / N-[(2H-1,3-benzodioxol-5-yl)methyl]-N-(1-propylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea


Mass: 463.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28F3N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.28 Å3/Da / Density % sol: 45.98 % / Mosaicity: 0.293 °
Crystal growTemperature: 277 K / Method: evaporation / Details: 6% PEG3350, 0.2M NH4Br

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 141508 / % possible obs: 94.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.024 / Rrim(I) all: 0.045 / Χ2: 0.757 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.11-1.143.20.29189230.8880.1890.3480.54589.6
1.14-1.163.40.24191310.9170.1530.2860.58892
1.16-1.23.30.19892110.9420.1270.2360.6193
1.2-1.233.10.16992130.9470.1120.2030.64393.1
1.23-1.273.40.14793020.9670.0930.1740.65893.7
1.27-1.323.40.12593430.9740.0790.1480.65794.3
1.32-1.373.30.10793920.980.0680.1270.65294.7
1.37-1.433.10.0994040.9840.0590.1080.67594.6
1.43-1.513.50.07694710.9890.0480.090.70295.4
1.51-1.63.40.06495860.9920.040.0750.71696.3
1.6-1.723.30.05595480.9930.0350.0650.77496.3
1.72-1.93.50.04696100.9960.0280.0540.85496.6
1.9-2.173.50.03897650.9970.0240.0451.03697.8
2.17-2.743.30.02997200.9980.0190.0351.02297.4
2.74-503.50.03298890.9940.020.0381.198.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LZM, 3TDU

2lzm

3tdu


Resolution: 1.1→49.172 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.19
RfactorNum. reflection% reflection
Rfree0.1723 7054 4.99 %
Rwork0.1456 --
obs0.1469 141464 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.12 Å2 / Biso mean: 20.177 Å2 / Biso min: 7.49 Å2
Refinement stepCycle: final / Resolution: 1.1→49.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 33 692 3684
Biso mean--14.76 32.63 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113134
X-RAY DIFFRACTIONf_angle_d1.3724251
X-RAY DIFFRACTIONf_chiral_restr0.08450
X-RAY DIFFRACTIONf_plane_restr0.008552
X-RAY DIFFRACTIONf_dihedral_angle_d12.7951216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1088-1.12140.21982060.20433821402781
1.1214-1.13460.19281970.17654277447490
1.1346-1.14840.2042250.16254325455092
1.1484-1.1630.18922830.15314328461192
1.163-1.17830.15212380.14744364460293
1.1783-1.19440.1632170.13954391460893
1.1944-1.21150.16862380.14014426466493
1.2115-1.22960.18772220.14114376459893
1.2296-1.24880.17032190.14084473469294
1.2488-1.26930.15932340.13814394462894
1.2693-1.29120.15412310.13694481471294
1.2912-1.31460.16952330.13694461469494
1.3146-1.33990.18282180.13734519473795
1.3399-1.36730.17792630.13784394465795
1.3673-1.3970.16892390.13944505474495
1.397-1.42950.17012310.14324457468895
1.4295-1.46530.16732420.14134523476595
1.4653-1.50490.17992170.13724525474296
1.5049-1.54920.18052610.13564522478396
1.5492-1.59920.15612290.13384596482596
1.5992-1.65630.15782070.13644578478596
1.6563-1.72260.16512470.14474564481196
1.7226-1.8010.162460.14634507475396
1.801-1.8960.17672500.14674618486898
1.896-2.01480.16672390.14574654489398
2.0148-2.17040.15622570.13734636489398
2.1704-2.38880.15892400.14194659489998
2.3888-2.73440.17552240.15034625484997
2.7344-3.44490.18152460.14854733497999
3.4449-49.22030.18252550.15264678493397

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