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Structure paper

TitlePanDDA analysis group deposition of ground-state model
Journal, issue, pagesTo Be Published
Publish dateDec 7, 2018 (structure data deposition date)
AuthorsTalon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. ...Talon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. / MacLean, E. / Renjie, Z. / Dias, A. / Brennan, P.E. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.05 - 2 Å
Structure data

PDB-5qkb:
Ground-state model of NUDT5 and corresponding apo datasets for PanDDA analysis
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-5qpc:
Crystal Structure of DCP2 (NUDT20) after initial refinement with no ligand modelled (structure $n)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-5qt3:
Ground state model of human erythroid-specific 5'-aminolevulinate synthase, ALAS2 - SGC Diamond Xchem fragment screening
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-5qu9:
PanDDA analysis group deposition of ground-state model of Kalirin/Rac1 screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-5r4f:
PanDDA analysis group deposition of ground-state model of ATAD2
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-5r4o:
PanDDA analysis group deposition of ground-state model of BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF
Method: X-RAY DIFFRACTION / Resolution: 1.05 Å

PDB-5r7w:
PanDDA analysis group deposition of ground-state model of INTERLEUKIN-1 BETA
Method: X-RAY DIFFRACTION / Resolution: 1.27 Å

PDB-5rhy:
PanDDA analysis group deposition of ground-state model of Zika Virus NS3 Helicase
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-5rji:
PanDDA analysis group deposition of ground-state model of PHIP
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rjj:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00023833
Method: X-RAY DIFFRACTION / Resolution: 1.151 Å

PDB-5rjk:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024661
Method: X-RAY DIFFRACTION / Resolution: 1.21 Å

PDB-5rjl:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024662
Method: X-RAY DIFFRACTION / Resolution: 1.31 Å

PDB-5rjm:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024671
Method: X-RAY DIFFRACTION / Resolution: 1.407 Å

PDB-5rjn:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024673
Method: X-RAY DIFFRACTION / Resolution: 1.435 Å

PDB-5rjo:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00023827
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

PDB-5rjp:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024672
Method: X-RAY DIFFRACTION / Resolution: 1.242 Å

PDB-5rjq:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024665
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-5rjr:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z45705015
Method: X-RAY DIFFRACTION / Resolution: 1.27 Å

PDB-5rjs:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z285642082
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-5rjt:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z404993336
Method: X-RAY DIFFRACTION / Resolution: 1.169 Å

PDB-5rju:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z57261895
Method: X-RAY DIFFRACTION / Resolution: 1.32 Å

PDB-5rjv:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z57190020
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-5rjw:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z256709556
Method: X-RAY DIFFRACTION / Resolution: 1.514 Å

PDB-5rjx:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z285782452
Method: X-RAY DIFFRACTION / Resolution: 1.291 Å

PDB-5rjy:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z383325512
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-5rjz:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z755044716
Method: X-RAY DIFFRACTION / Resolution: 1.275 Å

PDB-5rk0:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z30932204
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rk1:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1507502062
Method: X-RAY DIFFRACTION / Resolution: 1.271 Å

PDB-5rk2:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z54633859
Method: X-RAY DIFFRACTION / Resolution: 1.235 Å

PDB-5rk3:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1501469697
Method: X-RAY DIFFRACTION / Resolution: 1.31 Å

PDB-5rk4:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z56791867
Method: X-RAY DIFFRACTION / Resolution: 1.284 Å

PDB-5rk5:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z57478994
Method: X-RAY DIFFRACTION / Resolution: 1.243 Å

PDB-5rk6:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194394
Method: X-RAY DIFFRACTION / Resolution: 1.241 Å

PDB-5rk7:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z31721097
Method: X-RAY DIFFRACTION / Resolution: 1.304 Å

PDB-5rk8:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z53116498
Method: X-RAY DIFFRACTION / Resolution: 1.272 Å

PDB-5rk9:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z461898648
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-5rka:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z126932614
Method: X-RAY DIFFRACTION / Resolution: 1.33 Å

PDB-5rkb:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z2004563941
Method: X-RAY DIFFRACTION / Resolution: 1.279 Å

PDB-5rkc:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z234898257
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rkd:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z2168282707
Method: X-RAY DIFFRACTION / Resolution: 1.237 Å

PDB-5rke:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z906021418
Method: X-RAY DIFFRACTION / Resolution: 1.291 Å

PDB-5rkf:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1674937530
Method: X-RAY DIFFRACTION / Resolution: 1.264 Å

PDB-5rkg:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1124201124
Method: X-RAY DIFFRACTION / Resolution: 1.282 Å

PDB-5rkh:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z31432917
Method: X-RAY DIFFRACTION / Resolution: 1.252 Å

PDB-5rki:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194396
Method: X-RAY DIFFRACTION / Resolution: 1.268 Å

PDB-5rkj:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z373768898
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-5rkk:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z275181224
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-5rkl:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1545196403
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-5rkm:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z2017168803
Method: X-RAY DIFFRACTION / Resolution: 1.28 Å

PDB-5rkn:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z373768900
Method: X-RAY DIFFRACTION / Resolution: 1.23 Å

PDB-5rko:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z30620520
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-5rkp:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1079512010
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-5rkq:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1545196101
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-5rkr:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1432018343
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-5rks:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1696844792
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rkt:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1266933824
Method: X-RAY DIFFRACTION / Resolution: 1.241 Å

PDB-5rku:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z32367954
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-5rkv:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z56877838
Method: X-RAY DIFFRACTION / Resolution: 1.277 Å

PDB-5rkw:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z27678561
Method: X-RAY DIFFRACTION / Resolution: 1.242 Å

PDB-5rkx:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1324080698
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rky:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1796014543
Method: X-RAY DIFFRACTION / Resolution: 1.38 Å

PDB-5rkz:
PanDDA analysis group deposition of ground-state model of human NUDT22 screened against the DSPL fragment library by X-ray Crystallography
Method: X-RAY DIFFRACTION / Resolution: 1.38 Å

PDB-5rob:
PanDDA analysis group deposition of ground-state model of SARS-CoV-2 helicase
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-5rw1:
PanDDA analysis group deposition of ground-state model of DHTKD1
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-5sds:
PanDDA analysis group deposition of ground-state model of Porphyromonas gingivalis DPP11
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-5smk:
PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NSP14
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7gtw:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster1
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-7gtx:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster2
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-7gty:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster3
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7gtz:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster5
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7gu0:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster6
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7gu1:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster7
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7gu2:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster8
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7gu3:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster9
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-7gu4:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster11
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7gu5:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster12
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-7gu6:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster14
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-7gu7:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster15
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7gu8:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster16
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7gu9:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster17
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-7gua:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster18
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7gub:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster19
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-7guc:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster20
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-HOH:
WATER / Water

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM / Dimethyl sulfoxide

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM / 2-Methyl-2,4-pentanediol

ChemComp-HH8:
4-bromanyl-1,8-naphthyridine

ChemComp-UUJ:
5-bromo-2-hydroxybenzonitrile

ChemComp-UUG:
(4-bromo-2-methoxyphenyl)methanol

ChemComp-UU1:
2-(4-bromo-1H-pyrazol-1-yl)ethan-1-ol

ChemComp-UUV:
4-bromo-1-(2-methoxyethyl)-1H-pyrazole

ChemComp-1P8:
6-bromo-1,3-dihydro-2H-indol-2-one

ChemComp-UUS:
4-bromo-1-(2-hydroxyethyl)pyridin-2(1H)-one

ChemComp-HHT:
2-(4-bromanyl-2-methoxy-phenyl)ethanoic acid

ChemComp-S9S:
~{N}-[2-(4-fluorophenyl)ethyl]methanesulfonamide

ChemComp-UUP:
N-cyclopropylpyrazolo[1,5-a]pyrimidine-3-carboxamide

ChemComp-UUM:
5-methyl-N-(1-methyl-1H-pyrazol-4-yl)-1,2-oxazole-3-carboxamide

ChemComp-O2D:
2-cyclohexyl-N-(4H-1,2,4-triazol-4-yl)acetamide

ChemComp-UVD:
methyl {4-[(pyridin-4-yl)methyl]phenyl}carbamate

ChemComp-60P:
3-methylthiophene-2-carboxylic acid

ChemComp-UVA:
N-methyl-2-(methylsulfonyl)aniline

ChemComp-UV7:
N-[(1H-pyrazol-4-yl)methyl]acetamide

ChemComp-K0J:
N-ethyl-1H-1,2,3-triazole-4-carboxamide

ChemComp-T0S:
N-[(4-sulfamoylphenyl)methyl]acetamide

ChemComp-UV1:
6-methoxy-1,3,4,5-tetrahydro-2H-1-benzazepin-2-one

ChemComp-UUY:
2-[methyl(pyridin-2-yl)amino]ethan-1-ol

ChemComp-UVV:
3-amino-1,6-dimethylpyridin-2(1H)-one

ChemComp-K1S:
N,N-diethyl-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-amine / antagonist*YM / Trapidil

ChemComp-UVS:
5-(methoxymethyl)-1,3,4-thiadiazol-2-amine

ChemComp-O1M:
4-(4-fluorophenyl)piperazine-1-carboxamide

ChemComp-UVM:
ethyl morpholine-4-carboxylate

ChemComp-UVJ:
3-(2-methyl-1H-benzimidazol-1-yl)propanamide

ChemComp-UVG:
N,N-dimethyl-1H-pyrazole-4-carboxamide

ChemComp-T6J:
2-[(methylsulfonyl)methyl]-1H-benzimidazole

ChemComp-UWG:
(1S)-1-(1-cyclopentyl-1H-pyrazol-4-yl)ethan-1-ol

ChemComp-UWD:
N-methyl-1-([1,2,4]triazolo[4,3-a]pyridin-3-yl)methanamine

ChemComp-UW7:
(6S)-1-methyl-4,5,6,7-tetrahydro-1H-benzotriazole-6-carboxylic acid

ChemComp-K2G:
5-chloro-2-(propan-2-yl)pyrimidine-4-carboxamide

ChemComp-UVY:
2-(1-ethyl-1H-pyrazol-4-yl)ethan-1-ol

ChemComp-GOJ:
ethyl 1~{H}-pyrazole-4-carboxylate

ChemComp-LPZ:
2-(4-methylphenoxy)-1-(4-methylpiperazin-4-ium-1-yl)ethanone

ChemComp-K2M:
4-(furan-2-carbonyl)piperazine-1-carboxamide

ChemComp-UWY:
N-(1-ethyl-1H-pyrazol-4-yl)cyclopentanecarboxamide

ChemComp-K0P:
N-[(1-ethyl-1H-pyrazol-4-yl)methyl]pyridine-3-carboxamide

ChemComp-UWV:
2-fluoro-N-[(1H-pyrazol-3-yl)methyl]aniline

ChemComp-O0V:
(2S)-2-[(3-fluoropyridin-2-yl)(methyl)amino]propan-1-ol

ChemComp-NUA:
N-(1-ethyl-1H-pyrazol-4-yl)cyclobutanecarboxamide

ChemComp-GX4:
cyclopropyl-[4-(4-fluorophenyl)piperazin-1-yl]methanone

ChemComp-UWS:
6-methyl-2-[(3-methyl-1,2-oxazol-5-yl)methyl]pyridazin-3(2H)-one

ChemComp-UXJ:
2-fluoro-N-[(3-methyl-1H-pyrazol-4-yl)methyl]aniline

ChemComp-O0G:
(2S)-2-[(5-chloro-3-fluoropyridin-2-yl)amino]propan-1-ol

ChemComp-UXG:
1-(diphenylmethyl)azetidin-3-ol

ChemComp-UXD:
(1H-pyrazol-4-yl)(pyrrolidin-1-yl)methanone

ChemComp-UXA:
~{N}-cyclopropyl-1,3-benzodioxole-5-carboxamide

ChemComp-YI6:
2-(4-ethoxyphenyl)ethanoic acid

ChemComp-UX7:
N-(6-methoxy-1,3-benzothiazol-2-yl)cyclopropanecarboxamide

ChemComp-UR1:
3-fluoro-5-methylbenzene-1-sulfonamide

ChemComp-UX1:
1-[(2-fluorophenyl)methyl]-N-methylcyclopropane-1-carboxamide

ChemComp-ZN:
Unknown entry

ChemComp-TPP:
THIAMINE DIPHOSPHATE / Thiamine pyrophosphate

Source
  • homo sapiens (human)
  • zika virus
  • severe acute respiratory syndrome coronavirus 2
  • porphyromonas gingivalis (bacteria)
KeywordsSGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / NUDT5 / HYDROLASE / TRANSFERASE / HYDROLASE/TRANSFERASE / HYDROLASE-TRANSFERASE complex / TRANSCRIPTION / BROMODOMAIN / BPTF / FALZ / FAC1 / BROMODOMAIN AND PHD FINGER-CONTAINING TRANSCRIPTION FACTOR / FETAL ALZ-50 CLONE 1 PROTEIN / SIGNALING PROTEIN / IL-1 BETA / VIRAL PROTEIN / PROTEIN BINDING / Fragment-based drug design / SAMPL7 / NUDIX domain / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 22 / OXIDOREDUCTASE / Diamond I04-1 fragment screening / peptidase / Porphyromonas gingivalis / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multiconformer

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