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- PDB-6xop: DCN1 bound to inhibitor 10 -

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Basic information

Entry
Database: PDB / ID: 6xop
TitleDCN1 bound to inhibitor 10
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-H9P / 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: 2.07 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,9282
Polymers44,3471
Non-polymers5811
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.868, 86.702, 126.234
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-H9P / N-[(1S)-1-cyclohexyl-2-{[(2S)-3-(1H-imidazol-1-yl)-2-methylpropanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide


Mass: 580.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H44N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
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: 2.07→50 Å / Num. obs: 23551 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.79 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Χ2: 0.953 / Net I/σ(I): 13.9 / Num. measured all: 166777
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.07-2.115.90.35611540.940.1590.390.887100
2.11-2.146.30.29911300.9620.1290.3260.9100
2.14-2.196.90.27111560.9680.110.2930.925100
2.19-2.237.30.22311460.9810.0880.240.951100
2.23-2.287.30.19511800.9830.0770.210.942100
2.28-2.337.30.16111400.9880.0640.1730.941100
2.33-2.397.30.14111640.9920.0560.1520.93100
2.39-2.457.40.12111620.9930.0480.130.924100
2.45-2.537.40.10511450.9950.0410.1130.936100
2.53-2.617.30.09111910.9960.0360.0980.916100
2.61-2.77.30.08111370.9970.0320.0870.968100
2.7-2.817.30.07611920.9960.030.0821.138100
2.81-2.947.30.06911560.9970.0270.0751.29100
2.94-3.097.30.06111920.9970.0240.0661.252100
3.09-3.297.30.04811580.9980.0190.0521.06100
3.29-3.547.20.03811890.9990.0150.0410.844100
3.54-3.97.10.04211970.9970.0170.0451.055100
3.9-4.4670.04112050.9980.0170.0441.088100
4.46-5.6270.0312390.9990.0120.0320.62199.9
5.62-506.40.02613180.9990.0110.0280.44999.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5v83


Resolution: 2.07→41 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.248 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1175 5 %RANDOM
Rwork0.198 ---
obs0.2 23490 99.9 %-
Displacement parametersBiso max: 117.87 Å2 / Biso mean: 30.95 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.0985 Å20 Å20 Å2
2---1.1757 Å20 Å2
3----1.9228 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.07→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 84 292 3194
Biso mean--34.52 35.83 -
Num. residues----356
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1036SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes525HARMONIC5
X-RAY DIFFRACTIONt_it2963HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion380SEMIHARMONIC5
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_contact3649SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2963HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4048HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion16.59
LS refinement shellResolution: 2.07→2.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2411 139 4.99 %
Rwork0.2134 2644 -
all0.2149 2783 -
obs--99.71 %
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)
12.6291-0.3642-1.29190-0.89530-0.00380.44210.01090.13120.1119-0.16280.2403-0.071-0.10810.12320.0856-0.0065-0.0592-0.0249-0.09769.41289.6228-13.1104
21.72971.0339-1.35252.1906-1.24882.1220.42050.0680.00670.472-0.20750.0907-0.5067-0.045-0.2130.13880.0624-0.0509-0.13160.0065-0.13914.60299.7048-5.2226
31.3224-0.53660.73991.9631-1.0841.60620.03930.01030.0212-0.0288-0.0213-0.08870.08660.0007-0.0179-0.0756-0.07660.0201-0.0578-0.0395-0.0875-6.34737.8899-39.2425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-6 - 20}A-6 - 20
2X-RAY DIFFRACTION2{A|24 - 1063}A24 - 1063
3X-RAY DIFFRACTION3{A|1064 - 1251}A1064 - 1251

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