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- PDB-6b5q: DCN1 bound to 38 -

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Basic information

Entry
Database: PDB / ID: 6b5q
TitleDCN1 bound to 38
Components
  • DCN1-like protein 1
  • Peptidomimetic Inhibitors DI-591
KeywordsLigase/Inhibitor / E3 ligase / complex / Ligase-Inhibitor complex / LIGASE
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 / Neddylation / nucleoplasm ...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 / Neddylation / 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 / EF-hand / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptidomimetic Inhibitors, (PPI)(CZS)(2KY)(MLY)(1XY) / TRIETHYLENE GLYCOL / DCN1-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsStuckey, J.
CitationJournal: J. Med. Chem. / Year: 2018
Title: High-Affinity Peptidomimetic Inhibitors of the DCN1-UBC12 Protein-Protein Interaction.
Authors: Zhou, H. / Zhou, W. / Zhou, B. / Liu, L. / Chern, T.R. / Chinnaswamy, K. / Lu, J. / Bernard, D. / Yang, C.Y. / Li, S. / Wang, M. / Stuckey, J. / Sun, Y. / Wang, S.
History
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DCN1-like protein 1
B: DCN1-like protein 1
D: Peptidomimetic Inhibitors DI-591
E: Peptidomimetic Inhibitors DI-591
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2556
Polymers53,9544
Non-polymers3002
Water1,982110
1
A: DCN1-like protein 1
D: Peptidomimetic Inhibitors DI-591
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1273
Polymers26,9772
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DCN1-like protein 1
E: Peptidomimetic Inhibitors DI-591
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1273
Polymers26,9772
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.087, 90.841, 105.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DCN1-like protein 1 / 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


Mass: 26251.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCUN1D1, DCUN1L1, RP42, SCCRO / Production host: Escherichia coli (E. coli) / References: UniProt: Q96GG9
#2: Protein/peptide Peptidomimetic Inhibitors DI-591


Class: Inhibitor / Mass: 725.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: Peptidomimetic Inhibitors, (PPI)(CZS)(2KY)(MLY)(1XY)
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 37 % PEG 300, 0.1 M phosphate-citrate pH 4.2 / PH range: 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 22799 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.019 / Rrim(I) all: 0.052 / Χ2: 0.755 / Net I/σ(I): 15.5 / Num. measured all: 168961
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.16-2.27.30.22611130.9810.090.2440.745100
2.2-2.247.50.1911310.990.0740.2040.71100
2.24-2.287.50.17211260.9920.0670.1850.691100
2.28-2.337.50.1511450.9930.0590.1610.693100
2.33-2.387.50.12511070.9960.0490.1350.679100
2.38-2.437.50.10511380.9960.0410.1130.64100
2.43-2.497.50.09511260.9960.0370.1020.665100
2.49-2.567.50.0811180.9970.0310.0860.652100
2.56-2.647.50.07211340.9980.0280.0770.65100
2.64-2.727.50.05911360.9980.0230.0630.618100
2.72-2.827.50.05311250.9990.0210.0570.612100
2.82-2.937.50.04411340.9990.0170.0480.593100
2.93-3.067.50.0411450.9990.0160.0430.561100
3.06-3.237.50.03811410.9990.0150.040.573100
3.23-3.437.50.03411360.9990.0130.0370.577100
3.43-3.697.50.03911550.9990.0150.0420.745100
3.69-4.067.40.05211490.9980.020.0561.36699.8
4.06-4.657.30.05811670.9960.0230.0621.747100
4.65-5.867.30.04311760.9980.0170.0461.00299.9
5.86-506.60.02811970.9990.0120.0310.56196.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→16.44 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.197
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1165 5.13 %RANDOM
Rwork0.195 ---
obs0.197 22721 99.2 %-
Displacement parametersBiso max: 154.67 Å2 / Biso mean: 57.05 Å2 / Biso min: 23.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.9654 Å20 Å20 Å2
2---10.6175 Å20 Å2
3---7.6521 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.16→16.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 214 110 3342
Biso mean--41.86 53.73 -
Num. residues----376
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1150SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes516HARMONIC5
X-RAY DIFFRACTIONt_it3319HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion403SEMIHARMONIC5
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_contact4010SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3319HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4582HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion18.05
LS refinement shellResolution: 2.16→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2439 169 5.84 %
Rwork0.2 2727 -
all0.2025 2896 -
obs--95.53 %
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)
10-0.42-1.09790.30134.104400.07010.2439-0.2339-0.08610.12940.20610.33220.0176-0.19960.2882-0.18610.1886-0.1715-0.22010.15873.2369.57831.6836
22.8475-0.1888-0.89223.97071.01375.1357-0.56970.3664-0.64440.0935-0.03520.41561.3231-0.28790.60480.0878-0.04910.268-0.3323-0.081-0.09265.063216.379111.6232
34.5573-3.9352-0.05164.5771-2.59230.6189-0.09660.0088-0.21290.2089-0.2123-0.30730.45510.19250.30890.54730.45590.2339-0.06610.16460.140317.769211.505619.3879
43.3625-0.41991.2811.40981.16975.8763-0.0988-0.0843-0.12040.1243-0.0181-0.03770.63630.52980.1170.00280.07590.0888-0.10490.0657-0.081211.87328.717826.5259
50-1.9274-0.14885.6602-2.25052.2796-0.0528-0.40280.14520.0597-0.1097-0.2409-0.28430.02690.16250.04530.0939-0.00630.0474-0.0510.02716.707438.203537.1529
63.4779-3.32613.11243.3599-0.91095.6953-0.26510.03660.78270.2344-0.1609-0.7767-0.11210.85930.426-0.2320.04830.0099-0.04760.1393-0.070120.440535.404533.6354
72.9045-0.9837-0.98660.52961.54414.80320.0411-0.43190.47460.4489-0.1231-0.44880.01660.10470.0820.12710.1673-0.064-0.0008-0.02040.030716.491737.520443.5707
80.31443.9889-0.66990.0511-0.62584.2118-0.0274-0.12990.03080.30330.2459-0.2945-0.15050.4259-0.2185-0.2863-0.4559-0.19370.65240.3815-0.250433.807644.558324.4042
94.87731.9847-0.41313.6389-0.42326.05590.2589-0.876-0.28880.4497-0.7626-0.5079-0.23581.63270.5037-0.3697-0.1296-0.08060.28820.3435-0.261528.528739.8914.5242
100.8359-1.7454-2.89610.54381.73545.3539-0.0438-0.0919-0.77950.0314-0.4909-0.34790.0780.84050.5348-0.36290.2898-0.01370.56390.45590.294335.069829.5469.4919
113.84740.5651-0.09126.7624-0.50764.02170.0948-0.1704-0.34610.2032-0.5119-0.25320.51650.42020.4171-0.11320.02520.0444-0.03450.1404-0.047216.903831.97187.0157
122.3083-0.7427-0.48753.57091.31553.34430.18390.52530.0269-0.626-0.5159-0.0398-0.06520.37010.3320.02030.12920.04570.08330.0691-0.085815.817736.0816-6.9246
132.5254-1.7868-3.3133.24014.36114.99880.2270.6809-0.2868-0.0745-0.61940.18330.401-0.22560.3924-0.05240.16590.03330.0393-0.0508-0.108511.385925.5348-6.2053
143.43020.21071.3535.46473.17046.30010.09630.5290.0947-0.2133-0.27190.45870.031-0.28670.1756-0.06330.2418-0.03280.1399-0.106-0.17637.694928.4573-13.3855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|62 - 71}A62 - 71
2X-RAY DIFFRACTION2{A|72 - 137}A72 - 137
3X-RAY DIFFRACTION3{A|138 - 150}A138 - 150
4X-RAY DIFFRACTION4{A|151 - 196}A151 - 196
5X-RAY DIFFRACTION5{A|197 - 205}A197 - 205
6X-RAY DIFFRACTION6{A|206 - 239}A206 - 239
7X-RAY DIFFRACTION7{A|240 - 251}A240 - 251
8X-RAY DIFFRACTION8{B|62 - 74}B62 - 74
9X-RAY DIFFRACTION9{B|75 - 133}B75 - 133
10X-RAY DIFFRACTION10{B|134 - 150}B134 - 150
11X-RAY DIFFRACTION11{B|151 - 172}B151 - 172
12X-RAY DIFFRACTION12{B|173 - 205}B173 - 205
13X-RAY DIFFRACTION13{B|206 - 233}B206 - 233
14X-RAY DIFFRACTION14{B|234 - 251}B234 - 251

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