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- PDB-7ulq: Recombinant Hannalgesin -

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Basic information

Entry
Database: PDB / ID: 7ulq
TitleRecombinant Hannalgesin
ComponentsLong neurotoxin OH-55
KeywordsBIOSYNTHETIC PROTEIN / recombinant / alpha neurotoxin / refolded
Function / homology
Function and homology information


envenomation resulting in modulation of receptor activity in another organism / acetylcholine receptor inhibitor activity / ion channel inhibitor activity / toxin activity / extracellular space
Similarity search - Function
Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake toxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / Alpha-elapitoxin-Oh3a
Similarity search - Component
Biological speciesOphiophagus hannah (king cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXu, J. / Lei, X. / Chen, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM064642 United States
CitationJournal: To Be Published
Title: Structure of recombinant Hannalgesin at 2.2 Angstroms resolution.
Authors: Xu, J. / Lei, X. / Li, S.X. / Chen, L.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Long neurotoxin OH-55
A: Long neurotoxin OH-55
C: Long neurotoxin OH-55
B: Long neurotoxin OH-55
F: Long neurotoxin OH-55
H: Long neurotoxin OH-55
D: Long neurotoxin OH-55
I: Long neurotoxin OH-55
J: Long neurotoxin OH-55
G: Long neurotoxin OH-55
K: Long neurotoxin OH-55
L: Long neurotoxin OH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,16317
Polymers96,72412
Non-polymers4395
Water3,027168
1
E: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
H: Long neurotoxin OH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2523
Polymers8,0601
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Long neurotoxin OH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1192
Polymers8,0601
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
I: Long neurotoxin OH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1522
Polymers8,0601
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
J: Long neurotoxin OH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1562
Polymers8,0601
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
G: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Long neurotoxin OH-55


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.509, 65.509, 164.752
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 10 or resid 12...
d_2ens_1(chain "B" and (resid 4 through 10 or resid 12...
d_3ens_1(chain "C" and (resid 4 through 10 or resid 12...
d_4ens_1(chain "D" and (resid 4 through 10 or resid 12...
d_5ens_1(chain "E" and (resid 4 through 10 or resid 12...
d_6ens_1(chain "F" and (resid 4 through 10 or resid 12...
d_7ens_1(chain "G" and (resid 4 through 10 or resid 12...
d_8ens_1(chain "I" and (resid 4 through 10 or resid 12...
d_9ens_1(chain "J" and (resid 4 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1CYSVALB3 - 9
d_12ens_1SERALAB11 - 29
d_13ens_1CYSTHRB31 - 32
d_14ens_1GLYPROB35 - 47
d_15ens_1LYSPROB50 - 67
d_21ens_1CYSVALD3 - 9
d_22ens_1SERALAD11 - 29
d_23ens_1CYSTHRD31 - 32
d_24ens_1GLYPROD35 - 47
d_25ens_1LYSPROD50 - 67
d_31ens_1CYSVALC3 - 9
d_32ens_1SERALAC11 - 29
d_33ens_1CYSTHRC31 - 32
d_34ens_1GLYPROC35 - 47
d_35ens_1LYSPROC50 - 67
d_41ens_1CYSVALG3 - 9
d_42ens_1SERALAG11 - 29
d_43ens_1CYSTHRG31 - 32
d_44ens_1GLYPROG35 - 47
d_45ens_1LYSPROG50 - 67
d_51ens_1CYSVALA3 - 9
d_52ens_1SERALAA11 - 29
d_53ens_1CYSTHRA31 - 32
d_54ens_1GLYPROA35 - 47
d_55ens_1LYSPROA50 - 67
d_61ens_1CYSVALE3 - 9
d_62ens_1SERALAE11 - 29
d_63ens_1CYSTHRE31 - 32
d_64ens_1GLYPROE35 - 47
d_65ens_1LYSPROE50 - 67
d_71ens_1CYSVALJ1 - 7
d_72ens_1SERALAJ9 - 27
d_73ens_1CYSTHRJ29 - 30
d_74ens_1GLYPROJ33 - 45
d_75ens_1LYSPROJ48 - 65
d_81ens_1CYSVALH3 - 9
d_82ens_1SERALAH11 - 29
d_83ens_1CYSTHRH31 - 32
d_84ens_1GLYPROH35 - 47
d_85ens_1LYSPROH50 - 67
d_91ens_1CYSVALI3 - 9
d_92ens_1SERALAI11 - 29
d_93ens_1CYSTHRI31 - 32
d_94ens_1GLYPROI35 - 47
d_95ens_1LYSPROI50 - 67

NCS oper:
IDCodeMatrixVector
1given(0.745043219612, 0.658533948792, -0.106036027832), (-0.655422915839, 0.752294120128, 0.0668906436957), (0.12382003999, 0.0196620220048, 0.992109874252)29.4806058671, 42.4698314057, 11.4266890983
2given(0.500712753628, 0.212423337134, -0.839144245166), (-0.815272354462, -0.210046230278, -0.539640221996), (-0.290891262165, 0.954335846014, 0.0680100478563)33.0059609805, 55.3777071088, 34.7239457404
3given(0.99777898465, -0.0233461532053, -0.0623863360083), (-0.0229520009584, -0.999711870432, 0.00702721628479), (-0.0625324191283, -0.0055797174857, -0.998027335954)-31.0820521154, 58.1277734526, 53.2740626682
4given(0.540500114802, 0.201566208464, -0.816841899944), (0.80018500576, 0.176792505766, 0.573104149751), (0.259929956826, -0.963387499146, -0.0657338880183)30.5825330783, -54.5209061387, 17.4898101287
5given(-0.0920650594912, -0.0331662110947, -0.995200496012), (0.965928933117, 0.239800966161, -0.0973488202069), (0.241878731988, -0.970255378274, 0.00995891268266)53.2000674044, -8.31952361187, 1.30146065405
6given(0.519753295714, 0.83765607898, -0.167895220127), (-0.837243263593, 0.538526121523, 0.0949385801744), (0.16994184053, 0.0912245021049, 0.981222635824)2.51965004907, 69.9452896482, 37.5199099977
7given(0.775488497886, 0.62193064004, -0.108719219208), (0.619868428068, -0.782705422709, -0.0559942242274), (-0.119919646139, -0.0239687346749, -0.992494220753)-3.28855951151, 16.5460349614, 40.0032668164
8given(0.88420553053, -0.464842035014, -0.0458526145919), (-0.459700032405, -0.883400301064, 0.0909933419961), (-0.0828037438012, -0.0593783678206, -0.994795330431)-18.3692771527, 29.1312838569, 83.4064034085

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Components

#1: Protein
Long neurotoxin OH-55 / CM-11


Mass: 8060.338 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ophiophagus hannah (king cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: Q53B58
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: rec-hannalgesin at 80 mg/ml in 200 mM NH4Ac (pH 7.0), 1:1 with 0.1 M Bis-Tris, 0.2 M (NH4)2SO4, 25% PEG3350, at 18 degree centigrade

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 0.999943 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999943 Å / Relative weight: 1
ReflectionResolution: 2.1→56.73 Å / Num. obs: 46141 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.061 / Rrim(I) all: 0.108 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3741 / CC1/2: 0.721 / Rpim(I) all: 0.611 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHENIX1.20.1_4487model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTN, 6ZFM
Resolution: 2.2→46.72 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.0721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 2073 5.17 %
Rwork0.2115 37994 -
obs0.2131 40067 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 25 168 6287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716258
X-RAY DIFFRACTIONf_angle_d1.00298552
X-RAY DIFFRACTIONf_chiral_restr0.0589978
X-RAY DIFFRACTIONf_plane_restr0.00851095
X-RAY DIFFRACTIONf_dihedral_angle_d11.95462264
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.455515365234
ens_1d_3BX-RAY DIFFRACTIONTorsion NCS1.31531922983
ens_1d_4BX-RAY DIFFRACTIONTorsion NCS0.540386626255
ens_1d_5BX-RAY DIFFRACTIONTorsion NCS1.46106834016
ens_1d_6BX-RAY DIFFRACTIONTorsion NCS1.31358985703
ens_1d_7BX-RAY DIFFRACTIONTorsion NCS0.539830535099
ens_1d_8BX-RAY DIFFRACTIONTorsion NCS0.509161147995
ens_1d_9BX-RAY DIFFRACTIONTorsion NCS0.65841582491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.35031340.2732567X-RAY DIFFRACTION99.52
2.25-2.310.29231400.25922494X-RAY DIFFRACTION99.7
2.31-2.370.28371680.24422548X-RAY DIFFRACTION99.78
2.37-2.440.27921260.24112558X-RAY DIFFRACTION99.81
2.44-2.520.30591780.26062480X-RAY DIFFRACTION99.85
2.52-2.610.30071380.26092498X-RAY DIFFRACTION99.92
2.61-2.710.28131340.23982543X-RAY DIFFRACTION99.89
2.71-2.840.24861220.25242567X-RAY DIFFRACTION99.96
2.84-2.990.27421180.26742573X-RAY DIFFRACTION100
2.99-3.170.23741360.23412512X-RAY DIFFRACTION99.96
3.17-3.420.27861020.21772581X-RAY DIFFRACTION100
3.42-3.760.24231270.19412537X-RAY DIFFRACTION100
3.76-4.30.20991580.18992527X-RAY DIFFRACTION100
4.31-5.420.2021540.16952528X-RAY DIFFRACTION100
5.42-46.720.23461380.18772481X-RAY DIFFRACTION98.24
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)
15.89591665635-1.695199485690.5802451661498.803084999361.935999840267.017190842780.1082122169860.0707114672235-0.238847110047-0.0580087724009-0.251363436274-0.2015578039680.408640234456-0.08396370021360.1466475893350.3910761212320.01485006152860.0624448413240.3025694267230.03093595356630.17870702475137.279765226-17.373762620115.2399456717
24.86379316734-0.7950555048172.45324385136.35876857531.180137678267.6410096688-0.2224849936920.415369764140.0205384586672-0.3373412480340.10713559432-0.227386098709-0.1430835134150.1844326763520.05875472429360.322842463075-0.0479907713-0.003009684718130.232082911418-0.01927805684840.24211972201232.953878104610.092968692515.7788787725
37.32506108694-0.287203165590.3229197247457.78233535081.575431907225.517001661560.1050950346920.190576331739-0.001501941841120.128016073565-0.243519209740.0254487580542-0.285839694233-0.07263436149830.1859876579810.568973322082-0.0177368954619-0.0921283532710.3941646238030.01878127869350.21346776858338.153911717817.906171080335.9229782678
44.871411702521.160428282640.06654891664688.760141749812.52178229558.6852997795-0.2160408307540.437086915945-0.200349368016-0.9397356734460.1887015709930.2147180564990.395991260592-0.446057235585-0.03374162750290.340242221032-0.124169529499-0.02500207540970.3457196072070.0166623465940.25403676840758.634831086429.633774240931.3350294294
59.57819857144-1.10821844855-0.396574470699.110981927880.0056964820780610.3118338408-0.1254176070250.28717493371-0.1985697770370.1806890288250.0140824734995-0.431261079403-0.576360143701-0.1526164416890.08369898190630.362587544739-0.0322389812722-0.03986225321090.3186337739720.01848572778070.18097153828733.958791183924.2241864-0.427902694722
64.990214875142.219672621971.813456528015.870004525731.1495249454910.2513228428-0.1580367851040.2502486297810.151699150151-0.1650679053730.178949915718-0.229514335056-0.2147504030321.133902465380.01604599412340.3197003721210.07079515917170.00565135782210.5738554649140.02442879878580.288402195331.7950800229733.103941656551.7850019346
77.023175637341.08553828828-1.158666549566.72645618173-1.117844449696.884568918430.10255622848-0.6698346373010.2419080012360.7614756309090.03576191394610.205077737342-0.724637658441-0.338423912211-0.1614135460250.4321106916810.009586702280840.01652063876440.297026048286-0.04702797318090.2413512334410.23161540073347.547103361535.4398662858
85.77781429845-1.32264252808-1.41432284864.845967901131.143431741397.464610798-0.515635848576-0.6055714654240.4926770465030.7907356886240.4798767173640.139021200616-1.23891501899-0.949633194874-0.02975449888040.8403245482750.317328151394-0.06975589515770.511276989786-0.06432974893140.30959226422326.522737879928.085675571720.1762709563
97.805599784780.06463210899842.029374786197.877272396231.00600705558.494752324720.007021903500980.01808162594840.08953790523570.1743152121830.0519453362396-1.32727874838-0.8699261974040.9889388158160.02166541660560.5061715493750.0270215702558-0.1356323224990.437596584002-0.06237295339790.6546075516465.102831328976.7484193487264.4548531426
106.945100621921.2323263388-1.247477298366.67039720468-1.61624078447.92789796704-0.07470122405030.360620886963-0.287928345739-0.8252045558680.459977385240.836842899494-0.0762751040846-1.23966781875-0.2582289061740.4386710165470.0122079449777-0.04068006835020.468731107866-0.1303170403450.58887460640725.177045875849.412212634259.8536940624
119.06237688259-0.147078158716-3.355562058745.144236547661.78375772547.765328698270.375886172151-0.09721051552060.3556601988330.956654081014-0.4835304141010.834250313366-0.699011229865-0.2666625422280.2105432018480.8800948793020.0373237147470.2488935156060.4828640752630.04518920948590.6905258309575.461549529163.1439178801725.9420500198
122.389070567642.410013897141.215642414124.220352315971.591952882227.85192695375-0.08202970712270.0499501674267-0.024529069343-0.399616351591-0.5001455742830.01921805295591.024982657820.2514258637980.3822618657871.214913694530.1640526138180.4974493465920.72339839294-0.08930587476411.000462202995.99526965653-1.2164620996943.0265501057
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain E and resseq 2:70)EA2 - 701 - 69
22(chain A and resseq 2:70)AB2 - 701 - 69
33(chain C and resseq 2:70)CC2 - 701 - 69
44(chain B and resseq 2:69)BD2 - 691 - 68
55(chain F and resseq 2:70)FE2 - 701 - 69
66(chain H and resseq 2:69)HF2 - 691 - 68
77(chain D and resseq 2:69)DG2 - 691 - 68
88(chain I and resseq 2:69)IH2 - 691 - 68
99(chain J and resseq 2:69)JI2 - 691 - 68
1010(chain G and resseq 4:69)GJ4 - 691 - 66
1111(chain K and resseq 3:69)KK3 - 691 - 67
1212(chain L and resseq 4:68)LL4 - 681 - 65

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