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- PDB-5c91: NEDD4 HECT with covalently bound indole-based inhibitor -

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Basic information

Entry
Database: PDB / ID: 5c91
TitleNEDD4 HECT with covalently bound indole-based inhibitor
ComponentsE3 ubiquitin-protein ligase NEDD4
Keywordsligase/ligase inhibitor / NEDD4 / HECT / LIGASE / INHIBITOR / ligase-ligase inhibitor complex
Function / homology
Function and homology information


formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / intracellular glucocorticoid receptor signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / intracellular glucocorticoid receptor signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / apicolateral plasma membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / proline-rich region binding / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / lysosomal transport / beta-2 adrenergic receptor binding / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / progesterone receptor signaling pathway / protein K63-linked ubiquitination / phosphoserine residue binding / regulation of macroautophagy / ubiquitin ligase complex / Downregulation of ERBB4 signaling / Regulation of PTEN localization / ubiquitin binding / regulation of membrane potential / receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / positive regulation of protein catabolic process / cellular response to UV / neuron projection development / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell cortex / ubiquitin-dependent protein catabolic process / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / protein domain specific binding / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
Chem-4YU / E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsSpan, I. / Smith, A.T. / Kathman, S. / Statsyuk, A.V. / Rosenzweig, A.C.
CitationJournal: J. Am. Chem. Soc. / Year: 2015
Title: A Small Molecule That Switches a Ubiquitin Ligase From a Processive to a Distributive Enzymatic Mechanism.
Authors: Kathman, S.G. / Span, I. / Smith, A.T. / Xu, Z. / Zhan, J. / Rosenzweig, A.C. / Statsyuk, A.V.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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: E3 ubiquitin-protein ligase NEDD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0552
Polymers44,7391
Non-polymers3161
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.200, 38.730, 60.360
Angle α, β, γ (deg.)90.000, 93.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 ubiquitin-protein ligase NEDD4 / Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down- ...Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down-regulated protein 4 / NEDD-4


Mass: 44739.031 Da / Num. of mol.: 1 / Fragment: unp residues 938-1312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4, KIAA0093, NEDD4-1, PIG53 / Production host: Escherichia coli (E. coli)
References: UniProt: P46934, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-4YU / methyl (2E)-4-{[(5-methoxy-1,2-dimethyl-1H-indol-3-yl)carbonyl]amino}but-2-enoate


Mass: 316.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, 35 mM calcium chloride, 5 mM TCEP, 6% PEG400
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.44→32.2 Å / Num. obs: 15105 / % possible obs: 98.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 23.03 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.071 / Net I/σ(I): 11.2 / Num. measured all: 47656
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.44-2.50.6022341810870.47298.7
10.91-32.20.01848.45661820.01493.7

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Processing

Software
NameVersionClassification
xia20.3.6.3data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XBF

2xbf


Resolution: 2.44→31.86 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.877 / SU B: 36.163 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.89 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2977 731 4.8 %RANDOM
Rwork0.2478 ---
obs0.2501 14371 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.45 Å2 / Biso mean: 50.376 Å2 / Biso min: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å2-0 Å2-1.09 Å2
2--1.63 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 2.44→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 23 7 3186
Biso mean--63.22 35.44 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193288
X-RAY DIFFRACTIONr_bond_other_d0.0010.023080
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.9514435
X-RAY DIFFRACTIONr_angle_other_deg0.71137077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9845378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89123.729177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78915590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0961523
X-RAY DIFFRACTIONr_chiral_restr0.0570.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
X-RAY DIFFRACTIONr_mcbond_it1.484.2151510
X-RAY DIFFRACTIONr_mcbond_other1.484.2171511
X-RAY DIFFRACTIONr_mcangle_it2.6186.3151888
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 55 -
Rwork0.361 1027 -
all-1082 -
obs--98.01 %
Refinement TLS params.Method: refined / Details: Chain A / Origin x: -22.8336 Å / Origin y: -2.3324 Å / Origin z: 8.9346 Å
111213212223313233
T0.2319 Å20.0084 Å20.0556 Å2-0.0077 Å2-0.0011 Å2--0.0293 Å2
L0.0864 °20.0248 °2-0.0193 °2-0.3101 °20.0308 °2--0.0107 °2
S-0.0198 Å °0.0234 Å °-0.0054 Å °0.0345 Å °0.0206 Å °-0.0608 Å °0.0302 Å °-0.0024 Å °-0.0008 Å °

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