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- PDB-7fyw: Crystal Structure of apo mouse FABP5, twinned in P21 with beta=90deg -

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Basic information

Entry
Database: PDB / ID: 7fyw
TitleCrystal Structure of apo mouse FABP5, twinned in P21 with beta=90deg
ComponentsFatty acid-binding protein 5
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding ...Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / long-chain fatty acid transmembrane transporter activity / fatty acid transport / Neutrophil degranulation / fatty acid binding / lipid metabolic process / glucose metabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / extracellular space / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
: / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of apo mouse FABP5
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein 5
B: Fatty acid-binding protein 5
C: Fatty acid-binding protein 5
D: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8025
Polymers61,7634
Non-polymers391
Water2,288127
1
A: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4802
Polymers15,4411
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein 5


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein 5


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid-binding protein 5


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.625, 75.128, 61.805
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fatty acid-binding protein 5 / Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / ...Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / Keratinocyte lipid-binding protein / Psoriasis-associated fatty acid-binding protein homolog / PA-FABP


Mass: 15440.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp5, Fabpe, Klbp, Mal1 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05816
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.473
ReflectionResolution: 1.83→42.98 Å / Num. obs: 25292 / % possible obs: 99.2 % / Redundancy: 6.36 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Rsym value: 0.083 / Χ2: 0.872 / Net I/σ(I): 10.02 / Num. measured all: 167736 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.81-1.866.2591.4491.2911792189618840.6891.58199.4
1.86-1.916.3981.0251.8711893187518590.751.11699.1
1.91-1.966.6210.7882.6412011182618140.8520.85699.3
1.96-2.026.7940.5083.7711835175017420.940.55199.5
2.02-2.096.60.4124.6311319172617150.9520.44899.4
2.09-2.166.5390.3155.7810744165416430.9690.34399.3
2.16-2.256.2610.2566.8610049161216050.9760.27999.6
2.25-2.346.390.2018.619751153315260.9870.2299.5
2.34-2.446.7410.1610.5410031149114880.9920.17499.8
2.44-2.566.6870.13312.479382140714030.9930.14599.7
2.56-2.76.4920.11214.128913137613730.9950.12299.8
2.7-2.866.1390.09916.037926129312910.9930.10999.8
2.86-3.066.2730.08318.987490119811940.9960.0999.7
3.06-3.36.5420.07121.887478114511430.9970.07799.8
3.3-3.626.330.06224.286659105310520.9970.06799.9
3.62-4.055.9090.05924.357029669650.9970.06599.9
4.05-4.675.7910.05425.2648768478420.9970.05999.4
4.67-5.726.2670.04926.2546317427390.9980.05499.6
5.72-8.095.6920.05224.5733075835810.9960.05799.7
8.09-42.9775.5630.0424.8719473563500.9980.04598.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_728refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.81→42.977 Å / FOM work R set: 0.7319 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.02 / Stereochemistry target values: TWIN_LSQ_F
Details: beautiful example of almost perfectly merohedrally twinned monoclinic form with beta=90deg, emulating orthorhombic symmetry. molecular replacement in 2mmm clashes for all space groups. ...Details: beautiful example of almost perfectly merohedrally twinned monoclinic form with beta=90deg, emulating orthorhombic symmetry. molecular replacement in 2mmm clashes for all space groups. pseudo-translation and anisotropy mask twinning statistics. effective resolution about 2.2A. extra residues at N-terminus engage in intermolecular beta-sheet to form non-native dimer.
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 2506 5.17 %RANDOM
Rwork0.2059 45997 --
obs0.208 48458 97.37 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.29 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 158.28 Å2 / Biso mean: 46.76 Å2 / Biso min: 17.27 Å2
Baniso -1Baniso -2Baniso -3
1--6.4695 Å20 Å20.3241 Å2
2--7.3693 Å2-0 Å2
3----0.8998 Å2
Refinement stepCycle: final / Resolution: 1.81→42.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 1 127 4372
Biso mean--41.4 31.75 -
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134298
X-RAY DIFFRACTIONf_angle_d0.9525761
X-RAY DIFFRACTIONf_chiral_restr0.061660
X-RAY DIFFRACTIONf_plane_restr0.003728
X-RAY DIFFRACTIONf_dihedral_angle_d15.7291616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8101-1.8470.37871470.39632624277191
1.847-1.88720.36491520.38952637278990
1.8872-1.93110.44961290.39832669279890
1.9311-1.97940.33061300.32282651278192
1.9794-2.03290.37781410.31572704284592
2.0329-2.09270.32321290.3182610273991
2.0927-2.16020.29691340.29322728286293
2.1602-2.23740.3211530.29612717287093
2.2374-2.3270.321420.28852649279191
2.327-2.43290.31731350.27182739287494
2.4329-2.56110.34431640.2562709287392
2.5611-2.72160.25391300.25462717284793
2.7216-2.93160.28071540.22872743289793
2.9316-3.22650.25661490.19962736288594
3.2265-3.6930.21321550.14932763291893
3.693-4.65150.1811510.11442769292094
4.6515-37.57210.21841540.15452832298694
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)
13.08090.37550.37652.43080.04772.3536-0.26440.5054-0.18210.14740.0777-0.1105-0.11330.05830.17910.0717-0.00130.00890.34070.01160.209117.6505-1.309921.6792
21.7286-0.52332.02980.8421-0.4713.7508-0.1571-0.18470.02920.2122-0.1068-0.1611-0.11590.0269-0.63640.1415-0.1311-0.04130.78990.09960.17227.3069-3.251420.8437
31.08550.8573-1.15276.19350.951.8510.3477-0.7456-0.4416-0.29570.02310.00760.1247-0.7176-0.23290.173-0.087-0.00230.6531-0.07840.232421.24410.1428.5618
43.84521.52682.32370.90920.8131.4452-0.1229-0.3075-0.04260.0521-0.32470.21130.0648-0.1060.12690.1913-0.1256-0.00830.7676-0.04090.286527.1495-3.667211.389
53.8108-2.39252.72593.4039-1.9333.73970.10781.3306-0.484-0.0452-0.2830.07320.47220.14210.17720.2494-0.0139-0.02840.5431-0.07640.344817.863-10.63719.5313
64.1567-0.40780.37285.6248-1.22453.807-0.05390.286-0.66710.18410.2243-0.27240.4314-0.5446-0.11650.1703-0.0294-0.03340.3525-0.10130.272613.5608-8.899616.6127
72.95762.0407-1.37327.3249-2.01412.97750.22790.2577-0.1020.8391-0.00210.1521-0.03680.0056-0.20360.33070.0222-0.05420.3696-0.06230.211716.2695-1.744423.8798
83.05950.2758-0.36911.5169-0.18255.53120.2243-0.5721-0.55640.40240.008-0.23630.2582-0.3939-0.20230.2295-0.016-0.08560.35580.06730.304227.311-5.774149.8536
96.84691.6396-2.51061.5012-1.52812.20790.1864-0.52070.8710.3860.15460.2259-0.3166-0.6917-0.16620.28780.17510.00290.8632-0.17740.329515.238212.304857.7317
104.4757-1.0226-1.08413.0132-0.00311.1214-0.1835-0.52090.0980.1070.18190.0955-0.05820.6215-0.00610.1586-0.0212-0.03340.4727-0.01540.183617.66750.280742.5494
113.04550.2062-0.05553.45740.94772.8984-0.2203-0.22660.75750.1621-0.00350.148-0.3804-0.01860.21340.1747-0.0521-0.04060.2512-0.11450.257926.11629.977343.7026
122.6581.7483-0.19543.4674-0.31993.0310.1-0.71260.11950.7018-0.0781-0.5663-0.05130.1247-0.03940.27670.0744-0.07410.3502-0.11650.20325.44282.044554.7892
134.51321.15690.47861.5757-0.46492.6164-0.2531-0.30190.6188-0.16640.12170.0572-0.4446-0.14660.15670.17690.0264-0.02690.2975-0.01410.347-2.50025.170937.0587
142.02520.92460.90130.57630.07221.14680.0170.1428-0.2534-0.28620.2302-0.06410.11180.0759-0.12810.6117-0.1865-0.24510.317-0.04610.5333-10.873-14.522729.4279
158.32781.54954.44952.07170.23056.60480.0331-0.6696-0.16330.64610.0892-0.32430.4684-0.1498-0.19770.31730.0649-0.02230.76550.03720.3537-19.2276-11.655628.0449
160.5770.6731-0.79653.68510.33181.6449-0.02330.78240.14630.03780.086-0.0880.18920.53780.02410.16940.0638-0.03370.57610.04880.2-12.1008-0.700544.0695
173.85861.48211.49854.7521.89585.88310.0216-0.7586-0.84480.4250.13420.54920.3247-0.4334-0.12960.3822-0.02360.00470.45620.20570.5782-8.2093-12.251546.7038
185.78526.65271.7068.91592.01872.68310.1475-0.6035-0.67120.42320.2516-0.42520.2959-0.3621-0.29050.30810.0566-0.03710.37240.07770.2438-1.8263-9.936946.1025
194.45820.76540.90316.5445-0.14483.19420.1692-0.2144-0.7938-0.0562-0.0785-0.03630.2889-0.1055-0.07260.2006-0.0213-0.07440.38320.05120.3243-1.3268-9.45139.7833
205.4955-2.7092-0.40767.02251.86355.05120.1890.78890.1378-0.9477-0.08970.2020.09120.4422-0.10740.3123-0.0455-0.12920.31430.06270.2304-4.2187-2.41331.9257
215.87971.8962.18264.17950.51120.8204-0.3374-0.1127-0.6297-0.3332-0.4620.05890.0408-0.76770.44750.2357-0.0423-0.04120.65960.0130.4142-22.521-7.776111.5116
221.554-0.54491.44856.2869-5.46625.3824-0.20260.3762-0.0203-0.94730.1423-0.170.9230.5934-0.02910.38260.04610.02470.64770.0080.1707-7.6762-4.51340.7733
233.94644.17221.89837.67742.08752.8567-0.01760.82720.4471-0.3910.4676-0.4092-0.31520.0453-0.32780.2199-0.07830.02530.52690.27630.6806-7.548112.2835-2.0587
249.4577-5.9186-3.5224.17731.31963.2371-0.1291-0.21441.86380.18921.5852-0.0566-0.8005-0.0822-1.38530.4635-0.00790.12650.69260.06930.60460.844610.8869-1.775
256.1580.3017-4.63833.2933-0.86644.8973-0.0341-0.62410.1644-0.14890.28980.1690.1254-0.4921-0.0540.1966-0.0224-0.09190.66070.03350.2332-7.9495-3.316912.1395
266.57430.2562-4.15091.04250.44526.3440.14640.0624-0.18380.11980.01-0.13430.17560.0408-0.25220.2001-0.0416-0.04270.6311-0.12230.2206-5.4658-0.300613.8304
274.28650.2961-5.4420.8287-0.48876.9266-0.1243-0.39810.1778-0.02090.03740.06160.0677-0.23790.09580.2517-0.0092-0.0270.4872-0.05390.2023-3.11993.356114.0207
286.06073.2973-1.61931.9574-1.87018.36180.2463-1.15640.66750.6144-0.7154-0.1926-0.8791.22460.34570.3464-0.0761-0.00050.37110.04350.4394-9.032711.079715.7293
293.7952.5763-2.56242.1839-2.27466.01730.2239-0.99010.90190.3260.06010.5638-0.5897-0.2271-0.16790.21990.10790.06780.4196-0.05320.366-15.69358.99515.022
304.01773.733-0.643.6308-1.38693.9569-0.0207-0.50240.52960.1352-0.1540.4908-0.4028-0.73690.18790.24090.03870.00580.3873-0.03670.2942-16.54369.355910.7513
313.9564-0.4469-0.71767.6997-0.88484.5025-0.0040.51810.3742-0.4712-0.02160.71570.1371-0.3460.06630.1594-0.0314-0.0070.26020.07370.2231-15.33244.79054.4428
324.0917-3.77772.89264.3485-4.16594.64230.09330.01230.0609-0.67860.1496-0.03880.4517-0.3708-0.26020.2962-0.0010.00620.430.00890.1913-11.66921.79740.1138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -3:28)A-3 - 28
2X-RAY DIFFRACTION2chain 'A' and (resseq 29:47)A29 - 47
3X-RAY DIFFRACTION3chain 'A' and (resseq 48:56)A48 - 56
4X-RAY DIFFRACTION4chain 'A' and (resseq 57:67)A57 - 67
5X-RAY DIFFRACTION5chain 'A' and (resseq 68:89)A68 - 89
6X-RAY DIFFRACTION6chain 'A' and (resseq 90:111)A90 - 111
7X-RAY DIFFRACTION7chain 'A' and (resseq 112:133)A112 - 133
8X-RAY DIFFRACTION8chain 'B' and (resseq -3:16)B-3 - 16
9X-RAY DIFFRACTION9chain 'B' and (resseq 17:37)B17 - 37
10X-RAY DIFFRACTION10chain 'B' and (resseq 38:67)B38 - 67
11X-RAY DIFFRACTION11chain 'B' and (resseq 68:111)B68 - 111
12X-RAY DIFFRACTION12chain 'B' and (resseq 112:133)B112 - 133
13X-RAY DIFFRACTION13chain 'C' and (resseq -3:16)C-3 - 16
14X-RAY DIFFRACTION14chain 'C' and (resseq 17:28)C17 - 28
15X-RAY DIFFRACTION15chain 'C' and (resseq 29:37)C29 - 37
16X-RAY DIFFRACTION16chain 'C' and (resseq 38:67)C38 - 67
17X-RAY DIFFRACTION17chain 'C' and (resseq 68:80)C68 - 80
18X-RAY DIFFRACTION18chain 'C' and (resseq 81:89)C81 - 89
19X-RAY DIFFRACTION19chain 'C' and (resseq 90:111)C90 - 111
20X-RAY DIFFRACTION20chain 'C' and (resseq 112:133)C112 - 133
21X-RAY DIFFRACTION21chain 'D' and (resseq -3:7)D-3 - 7
22X-RAY DIFFRACTION22chain 'D' and (resseq 8:16)D8 - 16
23X-RAY DIFFRACTION23chain 'D' and (resseq 17:25)D17 - 25
24X-RAY DIFFRACTION24chain 'D' and (resseq 26:37)D26 - 37
25X-RAY DIFFRACTION25chain 'D' and (resseq 38:49)D38 - 49
26X-RAY DIFFRACTION26chain 'D' and (resseq 50:57)D50 - 57
27X-RAY DIFFRACTION27chain 'D' and (resseq 58:67)D58 - 67
28X-RAY DIFFRACTION28chain 'D' and (resseq 68:80)D68 - 80
29X-RAY DIFFRACTION29chain 'D' and (resseq 81:89)D81 - 89
30X-RAY DIFFRACTION30chain 'D' and (resseq 90:99)D90 - 99
31X-RAY DIFFRACTION31chain 'D' and (resseq 100:121)D100 - 121
32X-RAY DIFFRACTION32chain 'D' and (resseq 122:133)D122 - 133

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