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- PDB-5uqv: USP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-... -

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Basic information

Entry
Database: PDB / ID: 5uqv
TitleUSP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl)phenol)
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HAUSP / USP7 / SBDD / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of circadian rhythm / regulation of protein stability / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / PML body / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / rhythmic process / p53 binding / Regulation of TP53 Degradation / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. ...ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Single Sheet / Papain-like cysteine peptidase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-8JM / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsMurray, J.M. / Rouge, L.
CitationJournal: Nature / Year: 2017
Title: USP7 small-molecule inhibitors interfere with ubiquitin binding.
Authors: Kategaya, L. / Di Lello, P. / Rouge, L. / Pastor, R. / Clark, K.R. / Drummond, J. / Kleinheinz, T. / Lin, E. / Upton, J.P. / Prakash, S. / Heideker, J. / McCleland, M. / Ritorto, M.S. / ...Authors: Kategaya, L. / Di Lello, P. / Rouge, L. / Pastor, R. / Clark, K.R. / Drummond, J. / Kleinheinz, T. / Lin, E. / Upton, J.P. / Prakash, S. / Heideker, J. / McCleland, M. / Ritorto, M.S. / Alessi, D.R. / Trost, M. / Bainbridge, T.W. / Kwok, M.C.M. / Ma, T.P. / Stiffler, Z. / Brasher, B. / Tang, Y. / Jaishankar, P. / Hearn, B.R. / Renslo, A.R. / Arkin, M.R. / Cohen, F. / Yu, K. / Peale, F. / Gnad, F. / Chang, M.T. / Klijn, C. / Blackwood, E. / Martin, S.E. / Forrest, W.F. / Ernst, J.A. / Ndubaku, C. / Wang, X. / Beresini, M.H. / Tsui, V. / Schwerdtfeger, C. / Blake, R.A. / Murray, J. / Maurer, T. / Wertz, I.E.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 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: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6154
Polymers84,9542
Non-polymers6612
Water00
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8072
Polymers42,4771
Non-polymers3301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8072
Polymers42,4771
Non-polymers3301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.788, 68.435, 76.739
Angle α, β, γ (deg.)90.000, 95.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 42476.953 Da / Num. of mol.: 2 / Fragment: UNP residues 192-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-8JM / 4-[2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl]phenol


Mass: 330.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18N4O

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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: 52.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 1000, 0.1M Tris-HCl 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→43.54 Å / Num. obs: 17893 / % possible obs: 96.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 93.74 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-ID% possible all
2.844-2.8533.80.4910.2920.572198.5
13.176-75.4453.30.020.0130.024192.3

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NB8

1nb8


Resolution: 2.84→43.54 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.905 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.446
RfactorNum. reflection% reflectionSelection details
Rfree0.293 919 5.15 %RANDOM
Rwork0.239 ---
obs0.242 17858 95.7 %-
Displacement parametersBiso max: 176.85 Å2 / Biso mean: 76.24 Å2 / Biso min: 43.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.8919 Å20 Å20.302 Å2
2---0.7998 Å20 Å2
3----0.0921 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 2.84→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 52 0 5384
Biso mean--64.76 --
Num. residues----658
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1956SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes164HARMONIC2
X-RAY DIFFRACTIONt_gen_planes776HARMONIC5
X-RAY DIFFRACTIONt_it5502HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion668SEMIHARMONIC5
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_contact5911SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5502HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7422HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion20.64
LS refinement shellResolution: 2.84→3.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.316 174 6.17 %
Rwork0.28 2646 -
all0.282 2820 -
obs--94.35 %

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