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- PDB-2nyr: Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin -

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Basic information

Entry
Database: PDB / ID: 2nyr
TitleCrystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin
ComponentsNAD-dependent deacetylase sirtuin-5
KeywordsHYDROLASE / HISTONE DEACETYLASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
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 / 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
Chem-SVR / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsMin, J.R. / Antoshenko, T. / Allali-Hassani, A. / Dong, A. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2007
Title: Structural basis of inhibition of the human NAD+-dependent deacetylase SIRT5 by suramin.
Authors: Schuetz, A. / Min, J. / Antoshenko, T. / Wang, C.L. / Allali-Hassani, A. / Dong, A. / Loppnau, P. / Vedadi, M. / Bochkarev, A. / Sternglanz, R. / Plotnikov, A.N.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionDec 19, 2006ID: 2FZQ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent deacetylase sirtuin-5
B: NAD-dependent deacetylase sirtuin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2815
Polymers58,8532
Non-polymers1,4283
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-58 kcal/mol
Surface area23130 Å2
MethodPISA
2
A: NAD-dependent deacetylase sirtuin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4922
Polymers29,4271
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: NAD-dependent deacetylase sirtuin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7893
Polymers29,4271
Non-polymers1,3632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.200, 116.205, 55.993
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent deacetylase sirtuin-5 / SIR2-like protein 5


Mass: 29426.521 Da / Num. of mol.: 2 / Fragment: Residues 34-302
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN / Suramin


Mass: 1297.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 200mM NaCl, 0.1M Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
211
ReflectionResolution: 2.06→58.12 Å / Num. all: 28096 / Num. obs: 28096 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.06→2.1 Å / % possible all: 86.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B4Y
Resolution: 2.06→58.12 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.642 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.293 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1402 5 %RANDOM
Rwork0.199 ---
all0.202 26667 --
obs0.202 26667 86.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.17 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.06→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 88 253 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224140
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9755631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2975513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41322.686175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90515636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2111534
X-RAY DIFFRACTIONr_chiral_restr0.2450.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023206
X-RAY DIFFRACTIONr_nbd_refined0.1880.21958
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.210
X-RAY DIFFRACTIONr_mcbond_it0.3311.52643
X-RAY DIFFRACTIONr_mcangle_it0.56224114
X-RAY DIFFRACTIONr_scbond_it0.81831767
X-RAY DIFFRACTIONr_scangle_it1.2554.51517
LS refinement shellResolution: 2.06→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 100 -
Rwork0.244 1900 -
obs--84.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
113.5323-7.1297-5.96125.73446.492713.1121-0.3518-1.1184-0.57920.42070.15860.1790.63790.27070.1933-0.02890.0421-0.050.0740.0459-0.044922.3207-0.742832.1323
20.24870.172-0.58011.50690.35671.76680.1882-0.1531-0.07480.0763-0.0596-0.13510.02020.0612-0.12860.0432-0.00480.01160.03690.01750.059920.2067-0.401219.0138
32.37432.5862-1.33293.3863-0.97651.1452-0.15350.11060.30830.0399-0.0018-0.07620.0653-0.1240.15540.00460.008-0.01680.08280.0410.10230.32762.264813.4464
49.37752.2475-0.13342.5976-0.22080.6997-0.11910.0925-0.32770.1819-0.06930.29960.4902-0.19670.18840.0181-0.00090.06850.04090.00730.0182-7.7067-3.47643.5892
52.2255-0.68281.14354.4972.18273.79630.0831-0.0734-0.2856-0.0562-0.21340.33060.2021-0.4350.1303-0.0006-0.02890.04310.03590.0120.0659-2.5534-1.2444-3.8642
615.34075.766-16.799713.7993.990534.17420.0913-1.03210.05860.89770.20750.27120.34820.7367-0.2988-0.00250.00170.02480.0139-0.03380.07432.32069.44752.8655
76.3891-0.84592.11712.73860.0652.0598-0.09010.07050.29720.0119-0.10750.0224-0.1152-0.10270.19760.0884-0.00350.0296-0.002-0.01270.046114.835610.697115.3307
85.77251.33182.40491.25770.15021.8898-0.0033-0.22190.15980.0246-0.0287-0.0802-0.11150.04920.0320.0195-0.00260.02120.0253-0.0250.079723.03243.213714.4775
919.06074.8384-0.69011.30750.46795.23850.00680.66480.7244-0.7147-0.00470.0194-0.0555-0.4172-0.00210.11110.07730.05780.05210.02950.068614.49878.11438.2577
101.46180.32710.86710.3899-0.71963.15020.06550.15170.0617-0.0309-0.13220.0495-0.00990.09940.06670.02660.04160.01650.00850.01120.036715.07042.45984.8867
114.8425-2.3423-2.95097.68494.65285.0449-0.03770.1351-0.0349-0.0965-0.0427-0.2349-0.07740.32950.08040.02360.0174-0.01370.01460.018-0.008710.93923.2731-7.9372
120.6009-2.0648-1.099611.72592.87152.18990.103-0.19650.4339-0.2639-0.0089-0.199-0.24220.0771-0.09410.00290.0195-0.00560.01540.01890.0619-1.193611.0143-8.2974
1317.13242.7094-7.79883.2123.037225.45170.0286-0.43250.0599-0.15860.00330.0710.5439-0.5889-0.0319-0.04320.03480.0147-0.04220.05130.0276-12.02625.9658-1.3856
1415.4762-4.244-5.33321.26621.95844.24010.17760.7085-0.0382-0.2927-0.09370.01740.0004-0.041-0.08390.0596-0.0056-0.01290.05130.0234-0.02913.09693.6027-15.8931
151.5932-2.11361.06212.8147-1.32061.445-0.16190.1071-0.3705-0.04350.0355-0.03890.2589-0.11830.12640.0157-0.0243-0.01040.04370.02410.05546.4374-2.7717-5.0198
1614.2959-0.14445.47380.04630.33755.5404-0.28770.0694-1.01140.11450.23240.18950.58650.11240.05530.13390.01550.0643-0.0737-0.05440.115510.3756-11.31261.4685
171.4092-1.71660.63552.331-0.29571.2409-0.04910.0452-0.116-0.0894-0.0648-0.08070.15350.21780.11390.0343-0.01420.0254-0.00620.00330.063621.7894-7.349914.0477
1811.5177-2.53126.40336.71630.02025.3932-0.07960.08610.01340.65230.0394-0.0578-0.03230.04720.04030.0742-0.04710.0196-0.02110.0024-0.027912.2143-11.209116.5676
194.4215-3.80250.34288.54930.28522.49270.0656-0.0461-0.59910.2162-0.14580.43080.3456-0.25410.08010.0603-0.0360.02910.0604-0.00110.014817.3604-7.998224.3772
200.68830.1242-0.42294.38481.08224.29330.0596-0.3883-0.02210.30610.0090.17910.19230.1019-0.06860.03220.01680.02470.06260.0014-0.002815.23562.617828.0288
218.690812.02059.936316.633114.071326.13790.93480.2531-2.86012.13352.2085-2.2615-0.3010.4655-3.14320.39580.37780.189-0.02050.01150.56-3.039-28.974535.2694
227.9207-5.6899-1.61576.9916-0.03551.4250.2027-0.0218-0.22870.5629-0.04390.2202-0.1773-0.0255-0.15880.09790.00750.0182-0.0185-0.002-0.00638.4342-32.714320.5594
235.6239-1.64430.92919.8750.39935.90150.0227-0.53030.30720.88560.0975-0.3618-0.18780.4366-0.12020.0005-0.0567-0.03890.0476-0.08170.034526.8061-28.765111.7417
244.772-1.03211.41381.97485.104517.13030.6153-0.10310.2708-0.51720.0896-0.8527-0.57390.1369-0.7050.0488-0.05810.1136-0.0714-0.00790.143423.5086-24.2556-0.7169
251.23470.5767-2.70086.3224-0.04756.15090.1007-0.0196-0.450.1292-0.0953-0.3251-0.23280.3485-0.0054-0.0196-0.0126-0.00920.021-0.03410.103622.6325-34.02563.0257
260.6241.2558-1.05494.7252-2.24391.7899-0.17450.0394-0.02210.04350.18240.09220.53170.1525-0.00790.06860.0148-0.0193-0.00220.00760.020110.9557-42.048316.3428
2717.76382.1839-1.56840.6010.67922.4252-0.391-0.8917-1.47420.59920.47551.03070.4589-0.4268-0.08450.0980.0440.2671-0.02870.22780.6308-8.3784-38.328123.7933
281.0345-1.9756-0.67333.8370.96812.0103-0.19440.2952-0.20110.32170.16990.46020.0117-0.12530.02460.0657-0.00130.0356-0.01690.01330.10054.6337-32.708615.1889
297.3476-7.0281.86322.1515-3.49653.0240.05070.7861-0.4296-0.5453-0.15351.01430.1138-0.00830.10280.0026-0.0315-0.0217-0.0066-0.03680.1480.7256-37.318613.281
300.74410.9994-0.4613.61771.05892.2064-0.10980.1162-0.0027-0.12950.03020.0092-0.084-0.20870.07960.03760.00080.00150.0073-0.00570.01479.2526-33.09650.2735
317.32241.40473.33850.98061.34742.225-0.1182-0.0819-0.28380.1020.2129-0.2504-0.0536-0.07-0.09470.0320.03450.0173-0.0303-0.0420.091823.4063-41.6476-1.0801
328.5973-2.467710.95810.7236-2.603833.1647-0.3733-0.1211.185-0.2052-0.2243-0.97520.18481.65170.5976-0.0749-0.0138-0.0260.1083-0.09180.247233.0213-35.861.1426
337.928-4.62225.18552.7099-3.07723.58420.3650.3262-0.1554-0.73620.0299-0.13540.1725-0.0055-0.39490.1853-0.02410.0390.0353-0.0639-0.014316.5257-34.523-11.9356
340.80580.1219-1.32195.37484.7626.76550.1776-0.01110.0566-0.3633-0.21310.002-0.28760.09320.03560.09670.01130.0085-0.0054-0.00650.053514.1189-25.59811.3446
3532.5672-3.1389-8.58611.0559-3.13698.213-0.05722.57410.8570.05860.19140.9121-0.4079-0.4598-0.1341-0.092-0.0164-0.07890.05480.04710.1266-0.7079-20.97839.3016
360.4968-1.7682-0.16186.3850.14172.0984-0.1513-0.20780.08780.70860.23060.3812-0.0181-0.1099-0.07930.10290.01340.0517-0.01380.02920.01283.8714-23.240921.1536
375.92191.2808-7.0281.9275-2.60789.0576-0.3370.43090.62240.60630.30960.6168-0.3568-0.47360.02740.08630.02970.0767-0.0081-0.00880.04961.832-17.373222.6022
382.05633.7571-0.03686.9466-0.7575.7871-0.232-1.5746-0.55971.38990.61120.2067-0.48860.4705-0.37920.42980.23420.12020.0266-0.0051-0.17595.2318-25.457729.7751
394.6092-9.7857-3.459924.308311.29317.0084-0.28450.4750.52690.98010.908-1.4449-1.0452-0.4201-0.62350.73340.18850.0953-0.12690.1039-0.26878.3837-29.111233.0901
4052.9671-5.6209-7.75117.9254-0.01431.77940.8238-1.4581-0.46561.6466-0.14930.82840.4308-0.4571-0.67450.310.08830.1152-0.06680.0795-0.10923.5914-37.739731.6819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA36 - 475 - 16
2X-RAY DIFFRACTION2AA48 - 6317 - 32
3X-RAY DIFFRACTION3AA64 - 7433 - 43
4X-RAY DIFFRACTION4AA75 - 8644 - 55
5X-RAY DIFFRACTION5AA87 - 10556 - 74
6X-RAY DIFFRACTION6AA106 - 10975 - 78
7X-RAY DIFFRACTION7AA110 - 12579 - 94
8X-RAY DIFFRACTION8AA126 - 14395 - 112
9X-RAY DIFFRACTION9AA144 - 148113 - 117
10X-RAY DIFFRACTION10AA149 - 164118 - 133
11X-RAY DIFFRACTION11AA165 - 178134 - 147
12X-RAY DIFFRACTION12AA179 - 186148 - 155
13X-RAY DIFFRACTION13AA187 - 197156 - 166
14X-RAY DIFFRACTION14AA198 - 213167 - 182
15X-RAY DIFFRACTION15AA214 - 222183 - 191
16X-RAY DIFFRACTION16AA223 - 229192 - 198
17X-RAY DIFFRACTION17AA230 - 251199 - 220
18X-RAY DIFFRACTION18AA252 - 262221 - 231
19X-RAY DIFFRACTION19AA263 - 277232 - 246
20X-RAY DIFFRACTION20AA286 - 302255 - 271
21X-RAY DIFFRACTION21BB36 - 515 - 20
22X-RAY DIFFRACTION22BB52 - 6821 - 37
23X-RAY DIFFRACTION23BB69 - 8438 - 53
24X-RAY DIFFRACTION24BB85 - 9554 - 64
25X-RAY DIFFRACTION25BB96 - 10565 - 74
26X-RAY DIFFRACTION26BB106 - 12275 - 91
27X-RAY DIFFRACTION27BB123 - 13392 - 102
28X-RAY DIFFRACTION28BB134 - 146103 - 115
29X-RAY DIFFRACTION29BB147 - 155116 - 124
30X-RAY DIFFRACTION30BB156 - 177125 - 146
31X-RAY DIFFRACTION31BB178 - 190147 - 159
32X-RAY DIFFRACTION32BB191 - 199160 - 168
33X-RAY DIFFRACTION33BB200 - 213169 - 182
34X-RAY DIFFRACTION34BB214 - 226183 - 195
35X-RAY DIFFRACTION35BB227 - 237196 - 206
36X-RAY DIFFRACTION36BB238 - 257207 - 226
37X-RAY DIFFRACTION37BB258 - 267227 - 236
38X-RAY DIFFRACTION38BB268 - 276237 - 245
39X-RAY DIFFRACTION39BB286 - 294255 - 263
40X-RAY DIFFRACTION40BB295 - 302264 - 271

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