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- PDB-5m5q: COPS5(2-257) IN COMPLEX WITH A AZAINDOLE (COMPOUND 4) -

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Basic information

Entry
Database: PDB / ID: 5m5q
TitleCOPS5(2-257) IN COMPLEX WITH A AZAINDOLE (COMPOUND 4)
ComponentsCOP9 signalosome complex subunit 5
KeywordsHYDROLASE / METAL PROTEASE / COP9 SIGNALOSOME / HYDROXYLASE
Function / homology
Function and homology information


macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / protein deneddylation / COP9 signalosome / metal-dependent deubiquitinase activity / protein neddylation ...macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / protein deneddylation / COP9 signalosome / metal-dependent deubiquitinase activity / protein neddylation / Hydrolases; Acting on peptide bonds (peptidases) / protein deubiquitination / regulation of JNK cascade / translation initiation factor activity / post-translational protein modification / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / positive regulation of DNA-binding transcription factor activity / metallopeptidase activity / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Neddylation / transcription coactivator activity / regulation of cell cycle / translation / chromatin / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cop9 signalosome subunit 5 C-terminal domain / Cop9 signalosome subunit 5 C-terminal domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
Similarity search - Domain/homology
Chem-7K1 / COP9 signalosome complex subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRenatus, M. / Altmann, E.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Azaindoles as Zinc-Binding Small-Molecule Inhibitors of the JAMM Protease CSN5.
Authors: Altmann, E. / Erbel, P. / Renatus, M. / Schaefer, M. / Schlierf, A. / Druet, A. / Kieffer, L. / Sorge, M. / Pfister, K. / Hassiepen, U. / Jones, M. / Ruedisser, S. / Ostermeier, D. / ...Authors: Altmann, E. / Erbel, P. / Renatus, M. / Schaefer, M. / Schlierf, A. / Druet, A. / Kieffer, L. / Sorge, M. / Pfister, K. / Hassiepen, U. / Jones, M. / Ruedisser, S. / Ostermeier, D. / Martoglio, B. / Jefferson, A.B. / Quancard, J.
History
DepositionOct 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2May 1, 2024Group: 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: COP9 signalosome complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6764
Polymers28,9511
Non-polymers7253
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-11 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.365, 102.365, 69.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein COP9 signalosome complex subunit 5 / / Signalosome subunit 5 / Jun activation domain-binding protein 1


Mass: 28950.980 Da / Num. of mol.: 1 / Fragment: UNP residues 2-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS5, CSN5, JAB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92905, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-7K1 / 1-[(3~{R})-3-(1~{H}-benzimidazol-2-yl)morpholin-4-yl]-3-[2-(4-methyl-2-phenyl-phenyl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]propan-1-one


Mass: 541.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H31N5O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 35% MPD, 0.2M LiSO4, 0,1 M Mes pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 18226 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 57.66 Å2 / Rsym value: 0.045 / Net I/σ(I): 22.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 2.2→21.73 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.219 929 5.1 %RANDOM
Rwork0.197 ---
obs0.198 18206 100 %-
Displacement parametersBiso mean: 68.84 Å2
Baniso -1Baniso -2Baniso -3
1--10.1623 Å20 Å20 Å2
2---10.1623 Å20 Å2
3---20.3247 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→21.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 50 47 1844
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011844HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.042492HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d626SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes258HARMONIC5
X-RAY DIFFRACTIONt_it1844HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion19.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion224SEMIHARMONIC5
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_contact2021SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.308 143 4.9 %
Rwork0.242 2775 -
all0.246 2918 -
obs--99.97 %

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