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- PDB-5dy5: Crystal structure of human Sirt2 in complex with a SirReal probe ... -

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Basic information

Entry
Database: PDB / ID: 5dy5
TitleCrystal structure of human Sirt2 in complex with a SirReal probe fragment
ComponentsNAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / hydrolase inhibitor complex
Function / homology
Function and homology information


cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / : / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / : / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / tubulin deacetylase activity / regulation of exit from mitosis / paranode region of axon / Schmidt-Lanterman incisure / NAD-dependent protein lysine deacetylase activity / positive regulation of fatty acid biosynthetic process / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / chromatin silencing complex / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / NAD-dependent histone deacetylase activity / juxtaparanode region of axon / positive regulation of oocyte maturation / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone deacetylase activity / histone acetyltransferase binding / positive regulation of execution phase of apoptosis / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / glial cell projection / positive regulation of cell division / NAD+ ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / negative regulation of protein catabolic process / mitotic spindle / autophagy / histone deacetylase binding / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / cellular response to oxidative stress / midbody / growth cone / cellular response to hypoxia / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5GR / (R,R)-2,3-BUTANEDIOL / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRumpf, T. / Gerhardt, S. / Einsle, O. / Jung, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationJu295/8-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Structure-Based Development of an Affinity Probe for Sirtuin 2.
Authors: Schiedel, M. / Rumpf, T. / Karaman, B. / Lehotzky, A. / Gerhardt, S. / Ovadi, J. / Sippl, W. / Einsle, O. / Jung, M.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4306
Polymers34,4171
Non-polymers1,0145
Water4,288238
1
A: NAD-dependent protein deacetylase sirtuin-2
hetero molecules

A: NAD-dependent protein deacetylase sirtuin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,86112
Polymers68,8332
Non-polymers2,02710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5010 Å2
ΔGint-10 kcal/mol
Surface area25760 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint7 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.150, 53.360, 83.590
Angle α, β, γ (deg.)90.00, 114.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent protein deacetylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 34416.727 Da / Num. of mol.: 1 / Fragment: UNP residues 56-356
Source method: isolated from a genetically manipulated source
Details: Gly53 originates from the TEV cleavage site His54 and Met55 originate from the NdeI restriction site of the vector
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Plasmid: modified pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codonplus RIPL
References: UniProt: Q8IXJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 243 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5GR / N-(5-{3-[(1-benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzyl}-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide


Mass: 557.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27N7O2S2
#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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 17.5 % (wt/v) PEG 3350, 0.1 M HEPES / PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→45.85 Å / Num. obs: 28744 / % possible obs: 97.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 1.9 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RMG

4rmg


Resolution: 1.95→45.85 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.885 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20495 1437 5 %RANDOM
Rwork0.18989 ---
obs0.19066 27288 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.184 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.66 Å2
2--0.54 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.95→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 65 238 2681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192509
X-RAY DIFFRACTIONr_bond_other_d0.0020.022385
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.983379
X-RAY DIFFRACTIONr_angle_other_deg0.9263.0015512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50823.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8861515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7442.5211201
X-RAY DIFFRACTIONr_mcbond_other0.7442.521199
X-RAY DIFFRACTIONr_mcangle_it1.3673.7731497
X-RAY DIFFRACTIONr_mcangle_other1.3663.7731498
X-RAY DIFFRACTIONr_scbond_it0.5832.5651308
X-RAY DIFFRACTIONr_scbond_other0.5832.5651309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0683.8091882
X-RAY DIFFRACTIONr_long_range_B_refined4.16620.7322966
X-RAY DIFFRACTIONr_long_range_B_other4.16520.7322967
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 96 -
Rwork0.342 1931 -
obs--94.37 %
Refinement TLS params.Method: refined / Origin x: -5.8533 Å / Origin y: 0.7468 Å / Origin z: 14.8862 Å
111213212223313233
T0.0537 Å20.0234 Å20.0005 Å2-0.0372 Å2-0.0099 Å2--0.0041 Å2
L0.7711 °2-0.2639 °20.0894 °2-0.0909 °2-0.0398 °2--0.4546 °2
S0.0267 Å °-0.0358 Å °0.0043 Å °-0.011 Å °0.007 Å °0 Å °-0.0944 Å °0.0295 Å °-0.0337 Å °

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