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- PDB-5uqx: USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphen... -

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Basic information

Entry
Database: PDB / ID: 5uqx
TitleUSP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl-[3,3'-bipyridine]-6-carboxamide)
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 / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / : / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / rhythmic process / Regulation of TP53 Degradation / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / protein ubiquitination / nuclear body / Ub-specific processing proteases / 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. / meprin and TRAF homology ...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-8JP / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 1.2Nov 15, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Oct 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)85,9654
Polymers85,2682
Non-polymers6972
Water4,234235
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9832
Polymers42,6341
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9832
Polymers42,6341
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.355, 67.533, 76.861
Angle α, β, γ (deg.)90.000, 96.990, 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: 42634.148 Da / Num. of mol.: 2 / Fragment: UNP residues 192-539
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-8JP / 6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl[3,3'-bipyridine]-6-carboxamide


Mass: 348.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
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: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→38.145 Å / Num. obs: 37714 / % possible obs: 96.8 % / Redundancy: 3.8 % / CC1/2: 0.595 / Rpim(I) all: 0.113 / Rrim(I) all: 0.211 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.234-2.24240.0160.5811.111196
10.362-76.3053.60.9850.0390.072194.1

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Processing

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

1nb8


Resolution: 2.23→38.145 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.66
RfactorNum. reflection% reflection
Rfree0.2234 1938 5.14 %
Rwork0.1879 --
obs0.1897 37714 82.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.9 Å2 / Biso mean: 53.678 Å2 / Biso min: 20.16 Å2
Refinement stepCycle: final / Resolution: 2.23→38.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5508 0 52 235 5795
Biso mean--40.74 49.15 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095679
X-RAY DIFFRACTIONf_angle_d0.9967657
X-RAY DIFFRACTIONf_chiral_restr0.067811
X-RAY DIFFRACTIONf_plane_restr0.006997
X-RAY DIFFRACTIONf_dihedral_angle_d16.5343417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0968-2.14920.31221470.25142264241175
2.1492-2.20730.26981600.22892627278785
2.2073-2.27230.27471500.2142692284288
2.2723-2.34560.25271560.21252662281887
2.3456-2.42940.26651400.20922666280686
2.4294-2.52670.25381360.21182609274585
2.5267-2.64170.25541530.21662501265481
2.6417-2.78090.26941240.2072623274785
2.7809-2.95510.26971470.20242637278485
2.9551-3.18310.23931360.20292587272383
3.1831-3.50330.24251220.19152482260480
3.5033-4.00970.21141200.16782571269182
4.0097-5.050.15821370.15182419255678
5.05-38.1510.18761100.1792436254675
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)
11.53980.8048-0.07141.69260.29911.50890.0718-0.0235-0.02690.2584-0.13120.23150.2321-0.00240.00010.362-0.07340.04460.31-0.00720.30417.93774.67991.3024
22.0342-0.6304-0.76121.0442-0.1866-0.91440.0012-0.23680.0350.21-0.0629-0.3890.1276-0.0761-0.00540.35-0.0062-0.07380.283-0.00420.343245.379714.67752.5778
32.35260.89-0.20412.90670.14030.60250.1005-0.02330.30440.2648-0.09590.2731-0.0714-0.07180.0060.2413-0.03250.02480.2497-0.03210.25120.591717.88020.076
42.3362-0.3455-0.37870.67950.2551.2656-0.3148-0.086-0.3891-0.16970.0774-0.15450.38880.107900.4252-0.01860.10030.35360.04230.354215.92596.456738.8172
51.87471.51560.2402-0.42470.21780.0036-0.1035-0.12230.509-0.0562-0.06150.53730.04530.0469-0.02460.35650.01-0.11680.3856-0.0190.6069-12.795115.566637.7606
62.4520.046-0.30822.3616-0.03340.7474-0.1425-0.06580.2049-0.1499-0.0848-0.0797-0.05550.1752-0.02130.26730.00980.00010.33670.01120.23812.934318.770440.6697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 209 through 325 )A209 - 325
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 436 )A326 - 436
3X-RAY DIFFRACTION3chain 'A' and (resid 437 through 554 )A437 - 554
4X-RAY DIFFRACTION4chain 'B' and (resid 208 through 325 )B208 - 325
5X-RAY DIFFRACTION5chain 'B' and (resid 326 through 429 )B326 - 429
6X-RAY DIFFRACTION6chain 'B' and (resid 430 through 555 )B430 - 555

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