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- PDB-6xon: DCN1 bound to inhibitor 9 -

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Basic information

Entry
Database: PDB / ID: 6xon
TitleDCN1 bound to inhibitor 9
ComponentsLysozyme DCN1-like protein 1 chimera
KeywordsLIGASE/LIGASE INHIBITOR / Inhibitor / LIGASE / 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 / cytosol / cytoplasm
Similarity search - Function
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-H9M / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsStuckey, J.A.
CitationJournal: Nat Commun / Year: 2021
Title: Selective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity.
Authors: Zhou, H. / Lu, J. / Chinnaswamy, K. / Stuckey, J.A. / Liu, L. / McEachern, D. / Yang, C.Y. / Bernard, D. / Shen, H. / Rui, L. / Sun, Y. / Wang, S.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,9192
Polymers44,3471
Non-polymers5721
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.444, 85.610, 125.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 44347.434 Da / Num. of mol.: 1 / Mutation: C54T,C97A,D127A,A146T,R154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, DCUN1D1, DCN1, DCUN1L1, RP42, SCCRO / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q96GG9, lysozyme
#2: Chemical ChemComp-H9M / (2S)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-4-(dimethylamino)-2-methylbutanamide


Mass: 571.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H49N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 28-33% PEG 3350, 0.2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 10535 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 51.29 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Χ2: 0.942 / Net I/σ(I): 8.7 / Num. measured all: 70332
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.756.80.7035100.8850.2890.7610.731100
2.75-2.86.70.6325370.8430.2620.6860.746100
2.8-2.856.80.5354950.9150.220.5790.835100
2.85-2.916.80.4335010.9320.1790.4690.787100
2.91-2.976.70.3945230.9230.1630.4270.877100
2.97-3.046.70.335260.9560.1370.3580.881100
3.04-3.126.80.2944990.9580.1210.3190.959100
3.12-3.26.70.2445020.9690.1010.2641.051100
3.2-3.36.70.1895450.9830.0790.2051.083100
3.3-3.46.70.1625150.9860.0680.1761.176100
3.4-3.526.70.1335040.9910.0550.1441.186100
3.52-3.666.60.1185250.9910.0490.1281.182100
3.66-3.836.60.15180.9940.0430.1091.25199.8
3.83-4.036.70.0855260.9960.0350.0921.12100
4.03-4.296.70.0785350.9960.0320.0841.141100
4.29-4.626.80.0665290.9960.0270.0720.994100
4.62-5.086.80.0555340.9970.0220.060.81100
5.08-5.816.80.0535430.9970.0210.0570.709100
5.81-7.326.70.0495560.9970.020.0530.613100
7.32-505.80.0556120.9960.0250.0610.75399.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V83

5v83


Resolution: 2.8→37.51 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.836 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.452
RfactorNum. reflection% reflectionSelection details
Rfree0.289 435 4.67 %RANDOM
Rwork0.221 ---
obs0.224 9324 99.2 %-
Displacement parametersBiso max: 112.51 Å2 / Biso mean: 42.25 Å2 / Biso min: 8.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.735 Å20 Å20 Å2
2---3.4223 Å20 Å2
3----0.3127 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.8→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 87 58 2924
Biso mean--42.73 31.34 -
Num. residues----349
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1031SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes509HARMONIC5
X-RAY DIFFRACTIONt_it2925HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion372SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3424SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2925HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3996HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.02
X-RAY DIFFRACTIONt_other_torsion19.11
LS refinement shellResolution: 2.8→2.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.4278 27 6.08 %
Rwork0.2479 417 -
all0.2592 444 -
obs--89.72 %
Refinement TLS params.Method: refined / Origin x: 1.7385 Å / Origin y: 8.7043 Å / Origin z: 24.0639 Å
111213212223313233
T-0.0049 Å2-0.0201 Å2-0.0096 Å2--0.0757 Å2-0.0057 Å2---0.0388 Å2
L0.4657 °2-0.2351 °20.6927 °2-0.3341 °20.0998 °2--1.6065 °2
S0.0534 Å °-0.0144 Å °-0.0466 Å °-0.0882 Å °0.0141 Å °-0.0256 Å °0.1364 Å °0.0954 Å °-0.0675 Å °
Refinement TLS groupSelection details: { A|* }

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