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- PDB-4ixh: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

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Basic information

Entry
Database: PDB / ID: 4ixh
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Cryptosporidium parvum
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold / TIM barrel
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / Chem-Q21 / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Kavitha, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Med.Chem. / Year: 2013
Title: Optimization of Benzoxazole-Based Inhibitors of Cryptosporidium parvum Inosine 5'-Monophosphate Dehydrogenase.
Authors: Gorla, S.K. / Kavitha, M. / Zhang, M. / Chin, J.E. / Liu, X. / Striepen, B. / Makowska-Grzyska, M. / Kim, Y. / Joachimiak, A. / Hedstrom, L. / Cuny, G.D.
History
DepositionJan 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Structure summary
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,36717
Polymers154,0264
Non-polymers3,34113
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22280 Å2
ΔGint-103 kcal/mol
Surface area44750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.185, 92.016, 92.139
Angle α, β, γ (deg.)90.00, 103.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 38506.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: 56k.02, cgd6_20 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BM21 Magic / References: UniProt: Q8T6T2, IMP dehydrogenase
#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-Q21 / (2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide


Mass: 409.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H19N3O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 90-134 ARE DELETED AND REPLACED WITH SGG LINKER

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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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 289 K / pH: 7
Details: 0.1 M succinic acid pH 7.0, 15 %(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 83034 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 28.6 Å2 / Rsym value: 0.119 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.66 / % possible all: 96.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3FFS
Resolution: 2.105→35.521 Å / SU ML: 0.22 / Isotropic thermal model: mixed / σ(F): 1.34 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 4141 4.99 %
Rwork0.1616 --
obs0.1641 82909 98.94 %
all-82909 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 2.105→35.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9888 0 236 486 10610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710427
X-RAY DIFFRACTIONf_angle_d1.10414077
X-RAY DIFFRACTIONf_dihedral_angle_d13.8293894
X-RAY DIFFRACTIONf_chiral_restr0.071659
X-RAY DIFFRACTIONf_plane_restr0.0041762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1053-2.12930.32271020.26022452X-RAY DIFFRACTION90
2.1293-2.15430.29571400.2462540X-RAY DIFFRACTION98
2.1543-2.18060.33281390.23572582X-RAY DIFFRACTION98
2.1806-2.20820.26161570.22862572X-RAY DIFFRACTION99
2.2082-2.23720.28971360.21652645X-RAY DIFFRACTION99
2.2372-2.26790.25951370.21452576X-RAY DIFFRACTION99
2.2679-2.30030.28121340.20592633X-RAY DIFFRACTION99
2.3003-2.33460.30021310.19742622X-RAY DIFFRACTION99
2.3346-2.37110.2531280.19752651X-RAY DIFFRACTION99
2.3711-2.40990.25171310.19722592X-RAY DIFFRACTION99
2.4099-2.45150.27921370.18892605X-RAY DIFFRACTION99
2.4515-2.49610.30221270.17762644X-RAY DIFFRACTION99
2.4961-2.5440.23951460.16662612X-RAY DIFFRACTION99
2.544-2.5960.20911330.17212606X-RAY DIFFRACTION99
2.596-2.65240.24921400.16062630X-RAY DIFFRACTION99
2.6524-2.71410.20631310.16482650X-RAY DIFFRACTION99
2.7141-2.78190.21141570.15322616X-RAY DIFFRACTION100
2.7819-2.85710.25291340.15592631X-RAY DIFFRACTION100
2.8571-2.94110.19391490.15692626X-RAY DIFFRACTION100
2.9411-3.0360.22561340.16462665X-RAY DIFFRACTION100
3.036-3.14450.1921430.15732634X-RAY DIFFRACTION100
3.1445-3.27030.22551410.15582649X-RAY DIFFRACTION100
3.2703-3.4190.24591340.15712671X-RAY DIFFRACTION100
3.419-3.59910.181300.14212658X-RAY DIFFRACTION100
3.5991-3.82430.19521340.14632666X-RAY DIFFRACTION100
3.8243-4.11920.17731400.13312651X-RAY DIFFRACTION100
4.1192-4.5330.17491370.12872653X-RAY DIFFRACTION100
4.533-5.18720.15941430.12412692X-RAY DIFFRACTION100
5.1872-6.52870.17771660.16592671X-RAY DIFFRACTION100
6.5287-35.52590.16471500.15752673X-RAY DIFFRACTION98
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)
12.14971.0615-2.29073.162-2.81835.7809-0.06130.12260.1103-0.0842-0.1158-0.04430.31920.15870.19920.07730.0373-0.00880.1562-0.00290.162534.1146-18.334-2.6038
21.1775-0.1587-0.22172.3961-1.22312.3336-0.0477-0.16290.14490.529-0.06540.3378-0.4322-0.13160.00180.34920.09540.07940.224-0.07280.274822.1647-1.82146.8192
31.79490.59620.12841.9646-0.02410.964-0.0565-0.11410.41870.05530.02680.6539-0.5176-0.2516-0.01140.45930.18870.01860.257-0.09260.421617.110411.96860.0573
43.6967-3.1869-2.95693.86773.97586.1564-0.01310.17390.4697-0.0917-0.0471-0.0713-0.1406-0.19140.03660.38040.0111-0.0810.1385-0.01370.237531.85812.4577-6.8566
51.0374-0.4456-0.10831.4636-0.40192.3152-0.0672-0.04220.1110.01950.0132-0.0509-0.2464-0.00240.06180.13530.0271-0.0040.1013-0.00050.159132.4385-2.6276-5.2026
63.6885-0.94390.04311.66180.0721.8875-0.06590.18980.0951-0.221-0.23020.5474-0.1818-0.65030.16440.26410.0935-0.0390.2944-0.10960.406611.0812-2.7788-10.4835
73.0804-0.8311-0.32372.8514-0.57211.77730.1413-0.44910.18940.8774-0.19680.3733-0.1546-0.16710.19110.30060.03020.13910.1998-0.0620.210123.8059-12.62249.3956
82.55040.9273-1.5423.0914-1.3764.3761-0.51030.4795-0.3485-0.35720.77250.81120.3935-1.12-0.34380.5194-0.00880.05580.39130.15550.530822.5579-26.8444-5.0301
90.9143-0.2805-0.03081.15630.77682.22540.06930.16430.1234-0.3428-0.0203-0.111-0.56990.0369-0.02330.2688-0.01290.01640.16390.01150.159437.9366-6.1555-29.9764
101.648-0.2557-0.20561.2083-0.07992.783-0.00850.39580.0654-0.59350.0004-0.0391-0.0401-0.08610.02220.54170.0150.03150.28540.04160.158936.6471-11.5564-52.0652
110.46610.09170.45472.28760.311.4780.01440.1534-0.0109-0.1385-0.02-0.0955-0.15590.02950.01290.22190.02970.01560.16540.01380.119937.5725-15.0748-35.2845
122.21240.0211-0.19423.9856-0.34052.6840.20510.268-0.24070.21430.37720.77090.002-0.9619-0.47640.422-0.0315-0.0530.61120.18810.380514.105-12.7522-42.5033
131.55990.63680.92141.95230.2782.62910.05180.20830.072-0.23910.09480.1427-0.0981-0.1667-0.08050.28830.062-0.0130.22540.06230.16427.984-8.7538-35.8548
145.5673-1.7872-1.42393.34280.63911.97880.1654-0.1471-0.70980.2681-0.37250.7559-0.4268-0.62980.30890.46540.03550.02160.4305-0.06480.312425.8409-13.3433-16.5921
151.4583-0.1612-0.57462.5603-2.22646.61930.154-0.1295-0.0496-0.049-0.1582-0.2712-0.2557-0.01970.02390.14750.00310.00440.1302-0.01110.196240.0717-33.5503-26.513
161.57930.5191-0.31752.5847-1.05052.779-0.0990.1722-0.2566-0.7748-0.03680.07050.51360.08290.13050.50760.0068-0.02730.2112-0.08610.219533.8828-50.8217-39.8069
172.62680.7369-0.26112.05711.33762.2060.04520.0974-0.3106-0.6307-0.07990.84830.7047-0.18460.07110.5957-0.0313-0.18720.2347-0.10180.421823.8699-62.0741-38.9727
182.6717-0.4895-0.05790.6843-0.35683.85870.03090.2775-0.6967-0.48950.06840.51070.25820.2699-0.02280.5419-0.0442-0.12070.203-0.09220.330130.5178-67.0196-32.7545
191.27390.6397-0.13633.29833.22923.69710.08450.0649-0.3178-0.0535-0.18370.07960.83550.00770.15470.47440.035-0.04620.1754-0.02050.28636.4268-64.4156-24.0564
204.67660.202-0.13647.73432.61764.2171-0.0723-0.0713-0.2954-0.1238-0.0006-0.45980.62330.2651-0.03860.20680.0512-0.02490.15640.02980.181841.5081-57.7479-24.0928
210.42920.4912-0.64092.1622-0.30732.74070.04160.0679-0.0872-0.1964-0.0270.02660.21290.0147-0.05280.17280.0158-0.03410.1405-0.02050.143835.3082-46.1836-26.241
224.3007-0.82222.78210.5613-0.41595.77410.0961-0.0229-0.3042-0.1555-0.26670.6325-0.018-0.84870.19440.4047-0.0228-0.11870.3531-0.1550.441813.0771-49.8938-31.172
232.4315-0.73912.12231.098-2.5667.9988-0.18530.0865-0.2792-0.15580.11980.33220.0012-0.4620.11170.47590.0231-0.21790.3156-0.16950.397215.7933-48.4436-27.2792
242.29261.4707-0.25163.6620.13972.63670.27740.4193-0.1768-0.8519-0.23190.09310.35350.15770.02330.34280.0636-0.0690.1547-0.04450.146636.6794-39.4001-41.8704
256.4117-2.24134.09262.0178-1.71154.5851-0.9894-0.34350.55510.05050.6320.1037-0.3486-1.29510.38460.47060.0346-0.03670.49550.04130.322828.6801-25.2751-29.7937
261.191.01110.40155.46332.68232.67430.0556-0.10230.1332-0.1131-0.11730.14420.107-0.03710.01810.07070.0086-0.01960.14330.01190.129434.8868-39.278-7.1399
271.158-0.22910.17942.21620.6721.95090.1228-0.1304-0.11330.27810.1576-0.05940.6134-0.56550.01960.3713-0.10840.07840.31720.10490.227522.18-49.70917.385
282.5933-0.3921-1.21521.25420.01432.17910.1427-0.239-0.10710.7739-0.01330.4540.7082-0.9324-0.00130.4147-0.18040.18460.59640.0750.322710.2629-46.563816.0554
293.97191.90290.45354.9856-0.25023.2392-0.189-0.2969-0.28990.76560.26650.04940.4182-0.4298-0.06040.4561-0.04060.13460.3860.05860.246116.6815-42.63122.7445
302.52581.1615-1.48934.3977-2.97672.77260.0563-0.37920.04520.38490.21020.1965-0.1497-0.3649-0.27290.4006-0.01330.09310.32340.0090.193924.9573-35.020122.0844
315.4292-0.231-1.03674.4811-3.70366.6477-0.0405-0.47430.02870.3617-0.0231-0.17970.5240.05450.07150.3079-0.03150.03560.1713-0.05460.113531.38-36.251216.8103
321.3151-0.4475-0.89762.83390.9321.7961-0.0011-0.2061-0.03050.21160.05390.00550.05590.0118-0.05280.1339-0.02540.03430.14520.0040.135429.2075-33.17556.1624
333.58910.59630.51621.8248-0.10712.00580.128-0.16420.0681-0.04570.06530.25930.0448-0.5417-0.15170.2257-0.04410.05680.23260.02090.175820.3665-42.57131.8239
344.5823.68351.57486.06461.48652.425-0.1019-0.09110.5201-0.35710.10210.5669-0.1492-0.65730.01620.2851-0.03890.09770.49020.12680.4045.743-33.24871.5127
355.42810.007-0.83371.61520.5231.50360.049-0.1228-0.45970.13970.10980.11470.7924-0.17850.01840.3101-0.1110.00330.15360.04910.200626.9645-52.3919-3.1764
366.29812.69094.18643.64482.41114.6491-0.37170.46070.4788-0.8964-0.20890.9843-0.5514-0.4270.7160.45050.0894-0.06270.3982-0.07520.387325.8214-38.6599-18.2108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 182 )
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 267 )
6X-RAY DIFFRACTION6chain 'A' and (resid 268 through 340 )
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 370 )
8X-RAY DIFFRACTION8chain 'A' and (resid 371 through 392 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 47 )
10X-RAY DIFFRACTION10chain 'B' and (resid 48 through 203 )
11X-RAY DIFFRACTION11chain 'B' and (resid 204 through 274 )
12X-RAY DIFFRACTION12chain 'B' and (resid 275 through 300 )
13X-RAY DIFFRACTION13chain 'B' and (resid 301 through 370 )
14X-RAY DIFFRACTION14chain 'B' and (resid 371 through 392 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 25 )
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 55 )
17X-RAY DIFFRACTION17chain 'C' and (resid 56 through 90 )
18X-RAY DIFFRACTION18chain 'C' and (resid 91 through 154 )
19X-RAY DIFFRACTION19chain 'C' and (resid 155 through 182 )
20X-RAY DIFFRACTION20chain 'C' and (resid 183 through 203 )
21X-RAY DIFFRACTION21chain 'C' and (resid 204 through 274 )
22X-RAY DIFFRACTION22chain 'C' and (resid 275 through 310 )
23X-RAY DIFFRACTION23chain 'C' and (resid 311 through 340 )
24X-RAY DIFFRACTION24chain 'C' and (resid 341 through 370 )
25X-RAY DIFFRACTION25chain 'C' and (resid 371 through 392 )
26X-RAY DIFFRACTION26chain 'D' and (resid 2 through 25 )
27X-RAY DIFFRACTION27chain 'D' and (resid 26 through 55 )
28X-RAY DIFFRACTION28chain 'D' and (resid 56 through 90 )
29X-RAY DIFFRACTION29chain 'D' and (resid 91 through 154 )
30X-RAY DIFFRACTION30chain 'D' and (resid 155 through 182 )
31X-RAY DIFFRACTION31chain 'D' and (resid 183 through 203 )
32X-RAY DIFFRACTION32chain 'D' and (resid 204 through 245 )
33X-RAY DIFFRACTION33chain 'D' and (resid 246 through 287 )
34X-RAY DIFFRACTION34chain 'D' and (resid 288 through 340 )
35X-RAY DIFFRACTION35chain 'D' and (resid 341 through 370 )
36X-RAY DIFFRACTION36chain 'D' and (resid 371 through 392 )

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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