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- PDB-7ms6: Structure of USP5 zinc-finger ubiquitin binding domain co-crystal... -

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Basic information

Entry
Database: PDB / ID: 7ms6
TitleStructure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (2-fluoro-4-((4-phenylpiperidin-1-yl)sulfonyl)benzoyl)glycine
ComponentsUbiquitin carboxyl-terminal hydrolase 5
KeywordsHYDROLASE/INHIBITOR / USP5 / ubiquitin / USP / ubiquitin specific protease / HYDROLASE / HYDROLASE-INHIBITOR complex
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 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-ZPV / Ubiquitin carboxyl-terminal hydrolase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsMann, M.K. / Zepeda-Velazquez, C.A. / Alvarez, H.G. / Dong, A. / Kiyota, T. / Aman, A. / Arrowsmith, C.H. / Al-Awar, R. / Harding, R.J. / Schapira, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Activity Relationship of USP5 Inhibitors.
Authors: Mann, M.K. / Zepeda-Velazquez, C.A. / Gonzalez-Alvarez, H. / Dong, A. / Kiyota, T. / Aman, A.M. / Loppnau, P. / Li, Y. / Wilson, B. / Arrowsmith, C.H. / Al-Awar, R. / Harding, R.J. / Schapira, M.
History
DepositionMay 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,1795
Polymers13,5351
Non-polymers6444
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Protein is monomeric in solution as tested by multiple orthogonal methods
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-9 kcal/mol
Surface area6420 Å2
Unit cell
Length a, b, c (Å)53.575, 53.575, 54.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 1 molecules A

#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.: 1 / Fragment: UNP residues 171-290
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, 141 molecules

#2: Chemical ChemComp-ZPV / N-[2-fluoro-4-(4-phenylpiperidine-1-sulfonyl)benzoyl]glycine


Mass: 420.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21FN2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 57.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M HEPES pH 7.5, 5% MPD

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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: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.55→38.1 Å / Num. obs: 22155 / % possible obs: 99.3 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.016 / Rrim(I) all: 0.047 / Net I/σ(I): 33.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.586.40.115691810820.9840.0490.12513.797.3
8.49-38.0770.06210021440.9930.0250.06747.899.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6NFT

6nft


Resolution: 1.55→38.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.833 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1638 1075 4.9 %RANDOM
Rwork0.1478 ---
obs0.1486 21067 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.82 Å2 / Biso mean: 12.457 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å20 Å2
2---0.22 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.55→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms858 0 39 137 1034
Biso mean--17.93 25.9 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013962
X-RAY DIFFRACTIONr_bond_other_d0.0010.017827
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.6271312
X-RAY DIFFRACTIONr_angle_other_deg1.6271.6221917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8222.552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.12315143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.786156
X-RAY DIFFRACTIONr_chiral_restr0.1140.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021193
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02223
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.162 137 -
Rwork0.149 1457 -
all-1594 -
obs--97.25 %

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