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- PDB-6eqs: Human Sirt5 in complex with stalled peptidylimidate intermediate ... -

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Basic information

Entry
Database: PDB / ID: 6eqs
TitleHuman Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29
ComponentsNAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsSIGNALING PROTEIN / Hydrolase / PTM / inhibitor
Function / homology
Function and homology information


protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein deacetylation / NAD-dependent histone deacetylase activity / negative regulation of cardiac muscle cell apoptotic process / NAD+ binding / negative regulation of reactive oxygen species metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrion organization / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / transferase activity / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / 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 III / 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
1,3-BUTANEDIOL / Chem-BV8 / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsPannek, M. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Oberfrankenstiftung04115 Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight.
Authors: Rajabi, N. / Auth, M. / Troelsen, K.R. / Pannek, M. / Bhatt, D.P. / Fontenas, M. / Hirschey, M.D. / Steegborn, C. / Madsen, A.S. / Olsen, C.A.
History
DepositionOct 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
B: NAD-dependent protein deacylase sirtuin-5, mitochondrial
C: NAD-dependent protein deacylase sirtuin-5, mitochondrial
D: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,44337
Polymers119,6524
Non-polymers6,79033
Water19,5641086
1
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,80512
Polymers29,9131
Non-polymers1,89211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,73911
Polymers29,9131
Non-polymers1,82610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4357
Polymers29,9131
Non-polymers1,5226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4637
Polymers29,9131
Non-polymers1,5506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.326, 55.969, 123.034
Angle α, β, γ (deg.)97.39, 99.29, 90.52
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA35 - 3018 - 274
21ARGARGBB35 - 3018 - 274
12ALAALAAA34 - 3017 - 274
22ALAALACC34 - 3017 - 274
13ALAALAAA34 - 3017 - 274
23ALAALADD34 - 3017 - 274
14ARGARGBB35 - 3018 - 274
24ARGARGCC35 - 3018 - 274
15ARGARGBB35 - 3018 - 274
25ARGARGDD35 - 3018 - 274
16ILEILECC29 - 3012 - 274
26ILEILEDD29 - 3012 - 274

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NAD-dependent protein deacylase sirtuin-5, mitochondrial / Regulatory protein SIR2 homolog 5 / SIR2-like protein 5


Mass: 29913.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 1119 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BV8 / 3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]carbonimidoyl]amino]propanoic acid


Mass: 1180.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H63N11O19P2S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / 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: 2.27 Å3/Da / Density % sol: 45.9 % / Description: rods and rod-bundles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 5% 1,3-butandiol
PH range: 5.0 - 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.32→43.77 Å / Num. obs: 227669 / % possible obs: 91.5 % / Redundancy: 2 % / CC1/2: 0.999 / Rrim(I) all: 0.059 / Net I/σ(I): 6.8
Reflection shellResolution: 1.32→1.4 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 35569 / CC1/2: 0.723 / Rrim(I) all: 0.959 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIY

3riy


Resolution: 1.32→43.77 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.488 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20856 2388 1.1 %RANDOM
Rwork0.16025 ---
obs0.16076 224952 91.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.373 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å23.38 Å2-2.91 Å2
2---1.76 Å20.81 Å2
3---4.1 Å2
Refinement stepCycle: 1 / Resolution: 1.32→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8313 0 440 1086 9839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.029576
X-RAY DIFFRACTIONr_bond_other_d0.0050.028794
X-RAY DIFFRACTIONr_angle_refined_deg2.8862.03413011
X-RAY DIFFRACTIONr_angle_other_deg1.8013.02320369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41851145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61222.26385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.724151389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.431586
X-RAY DIFFRACTIONr_chiral_restr0.2760.21407
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02110362
X-RAY DIFFRACTIONr_gen_planes_other0.010.022049
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_it7.2791.7174446
X-RAY DIFFRACTIONr_mcbond_other7.2781.7174447
X-RAY DIFFRACTIONr_mcangle_it8.7622.5975560
X-RAY DIFFRACTIONr_mcangle_other8.7622.5975561
X-RAY DIFFRACTIONr_scbond_it7.1022.1585130
X-RAY DIFFRACTIONr_scbond_other7.1012.1595131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7663.0587426
X-RAY DIFFRACTIONr_long_range_B_refined9.45122.75710680
X-RAY DIFFRACTIONr_long_range_B_other9.45122.76510681
X-RAY DIFFRACTIONr_rigid_bond_restr6.781318370
X-RAY DIFFRACTIONr_sphericity_free47.725674
X-RAY DIFFRACTIONr_sphericity_bonded19.296518509
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A172600.07
12B172600.07
21A171420.09
22C171420.09
31A170620.09
32D170620.09
41B171680.09
42C171680.09
51B170280.09
52D170280.09
61C174520.08
62D174520.08
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 175 -
Rwork0.334 16405 -
obs--90.2 %

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