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- PDB-5ufi: DCN1 bound to DI-591 -

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Basic information

Entry
Database: PDB / ID: 5ufi
TitleDCN1 bound to DI-591
ComponentsDCN1-like protein 1
KeywordsLigase/Inhibitor / E3 ligase / complex / 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 / 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
N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide / Chem-8B1 / DCN1-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsStuckey, J.
CitationJournal: Nat Commun / Year: 2017
Title: A potent small-molecule inhibitor of the DCN1-UBC12 interaction that selectively blocks cullin 3 neddylation.
Authors: Zhou, H. / Lu, J. / Liu, L. / Bernard, D. / Yang, C.Y. / Fernandez-Salas, E. / Chinnaswamy, K. / Layton, S. / Stuckey, J. / Yu, Q. / Zhou, W. / Pan, Z. / Sun, Y. / Wang, S.
History
DepositionJan 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: DCN1-like protein 1
D: DCN1-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3518
Polymers105,0074
Non-polymers2,3434
Water72140
1
A: DCN1-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8382
Polymers26,2521
Non-polymers5861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DCN1-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8382
Polymers26,2521
Non-polymers5861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DCN1-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8382
Polymers26,2521
Non-polymers5861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DCN1-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8382
Polymers26,2521
Non-polymers5861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.142, 101.647, 173.521
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
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.: 4 / Fragment: UNP residues 58-259
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: Chemical
ChemComp-8B1 / N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 585.801 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H47N5O4S
References: N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 4000 and 100 mM potassium phosphate (monobasic)

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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: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.58→45.24 Å / Num. obs: 35513 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.039 / Rrim(I) all: 0.093 / Χ2: 0.929 / Net I/σ(I): 8 / Num. measured all: 188478
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.58-2.625.20.6160.836199.7
2.62-2.675.40.5630.908199.9
2.67-2.725.40.5020.9091100
2.72-2.785.40.450.9291100
2.78-2.845.40.3450.9531100
2.84-2.915.40.3030.9681100
2.91-2.985.40.2650.9691100
2.98-3.065.40.2150.9791100
3.06-3.155.40.1730.9861100
3.15-3.255.40.1540.9891100
3.25-3.375.40.1150.9931100
3.37-3.55.40.0920.9961100
3.5-3.665.40.0690.9971100
3.66-3.855.40.0560.9981100
3.85-4.095.30.0470.9981100
4.09-4.415.30.0450.9981100
4.41-4.855.30.0470.9971100
4.85-5.565.20.050.997199.8
5.56-75.20.0450.997199.9
7-504.80.0190.999198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2.58→45.24 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.443 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.431 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1758 4.98 %RANDOM
Rwork0.21 ---
obs0.211 35332 99.8 %-
Displacement parametersBiso max: 128.72 Å2 / Biso mean: 43.79 Å2 / Biso min: 12.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.386 Å20 Å20 Å2
2---0.0528 Å20 Å2
3---1.4387 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.58→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 165 40 6417
Biso mean--33.42 30.31 -
Num. residues----769
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3092SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes202HARMONIC2
X-RAY DIFFRACTIONt_gen_planes971HARMONIC5
X-RAY DIFFRACTIONt_it6565HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion815SEMIHARMONIC5
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_contact7479SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6565HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8880HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion3.13
LS refinement shellResolution: 2.58→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.312 128 4.59 %
Rwork0.239 2661 -
all0.242 2789 -
obs--98.28 %
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)
11.6120.43411.2321.06090.49983.6302-0.15610.00290.2429-0.01630.04690.0491-0.18170.0090.1093-0.0809-0.0111-0.0131-0.12410.0757-0.08390.51228.59943.6818
21.1189-0.25191.02281.1993-0.4543.46380.04750.00850.0440.0518-0.04560.0028-0.18460.0192-0.0018-0.071-0.01360.0273-0.0833-0.0444-0.1285-0.251415.5768-2.6923
33.7953-0.3472-0.24611.76960.23091.52220.00210.0026-0.1164-0.01930.1103-0.21830.11770.0632-0.1125-0.1054-0.0435-0.0267-0.15210.0355-0.11310.183-13.604847.437
43.103-0.4041-0.56731.93470.30031.8896-0.05140.03-0.42870.1786-0.01590.23350.3130.00060.0673-0.12750.00250.033-0.1363-0.0293-0.1365-0.1563-6.7429-6.2465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|60 - 251}A60 - 251
2X-RAY DIFFRACTION2{B|60 - 251}B60 - 251
3X-RAY DIFFRACTION3{C|60 - 251}C60 - 251
4X-RAY DIFFRACTION4{D|60 - 251}D60 - 251

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