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- PDB-6nft: Structure of USP5 zinc-finger ubiquitin binding domain co-crystal... -

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Basic information

Entry
Database: PDB / ID: 6nft
TitleStructure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-yl)acetic acid
ComponentsUbiquitin carboxyl-terminal hydrolase 5
KeywordsHYDROLASE / USP5 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein K48-linked deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / protein ubiquitination / Ub-specific processing proteases ...protein K48-linked deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / protein ubiquitination / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / Ubiquitin specific protease (USP) domain signature 2. ...Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / 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 associated domain / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(4-oxoquinazolin-3(4H)-yl)acetic acid / Ubiquitin carboxyl-terminal hydrolase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsHarding, R.J. / Mann, M.K. / Tempel, W. / Bountra, C. / Arrowmsmith, C.M. / Edwards, A.M. / Schapira, M. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)432008-2013 Canada
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain.
Authors: Mann, M.K. / Franzoni, I. / de Freitas, R.F. / Tempel, W. / Houliston, S. / Smith, L. / Vedadi, M. / Arrowsmith, C.H. / Harding, R.J. / Schapira, M.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 5
B: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,79626
Polymers27,0702
Non-polymers72524
Water4,414245
1
A: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,86715
Polymers13,5351
Non-polymers33214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,92911
Polymers13,5351
Non-polymers39410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.870, 85.040, 59.840
Angle α, β, γ (deg.)90.000, 99.000, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-305-

UNX

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ubiquitin carboxyl-terminal hydrolase 5 / Deubiquitinating enzyme 5 / Isopeptidase T / Ubiquitin thioesterase 5 / Ubiquitin-specific- ...Deubiquitinating enzyme 5 / Isopeptidase T / Ubiquitin thioesterase 5 / Ubiquitin-specific-processing protease 5


Mass: 13535.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP5, ISOT / Production host: Escherichia coli (E. coli) / References: UniProt: P45974, ubiquitinyl hydrolase 1

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Non-polymers , 5 types, 269 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-KKG / (4-oxoquinazolin-3(4H)-yl)acetic acid


Mass: 204.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8N2O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2 M sodium/potassium phosphate pH 7.0, 1.1% DMSO (v/v), 25% ethylene glycol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→26.94 Å / Num. obs: 36423 / % possible obs: 99.2 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.048 / Rrim(I) all: 0.097 / Net I/σ(I): 10.7 / Num. measured all: 147086
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.683.90.91617550.5910.5321.06497.7
9.04-26.943.70.0312300.9980.0180.03696.8

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.65→26.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.708 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 1821 5 %RANDOM
Rwork0.1802 ---
obs0.1816 34601 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.83 Å2 / Biso mean: 17.248 Å2 / Biso min: 1.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-0.56 Å2
2--0.61 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.65→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 61 245 2093
Biso mean--20.26 28.42 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131930
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171675
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6372622
X-RAY DIFFRACTIONr_angle_other_deg1.5021.5923887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95522.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9681511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02408
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 142 -
Rwork0.251 2484 -
all-2626 -
obs--97.66 %

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