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- PDB-2gcg: Ternary Crystal Structure of Human Glyoxylate Reductase/Hydroxypy... -

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Basic information

Entry
Database: PDB / ID: 2gcg
TitleTernary Crystal Structure of Human Glyoxylate Reductase/Hydroxypyruvate Reductase
ComponentsGlyoxylate reductase/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / NAD(P) Rossmann Fold / Formate/Glycerate Dehydrogenase Substrate-Binding Domain
Function / homology
Function and homology information


dicarboxylic acid metabolic process / glycerate dehydrogenase (NAD+) activity / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase [NAD(P)] activity / glyoxylate reductase (NADPH) activity / glyoxylate metabolic process / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process ...dicarboxylic acid metabolic process / glycerate dehydrogenase (NAD+) activity / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase [NAD(P)] activity / glyoxylate reductase (NADPH) activity / glyoxylate metabolic process / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process / peroxisomal matrix / catalytic complex / NADPH binding / NAD binding / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-2,3-DIHYDROXYPROPANOIC ACID / Chem-NDP / Glyoxylate reductase/hydroxypyruvate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBooth, M.P.S. / Conners, R. / Rumsby, G. / Brady, R.L.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural basis of substrate specificity in human glyoxylate reductase/hydroxypyruvate reductase
Authors: Booth, M.P.S. / Conners, R. / Rumsby, G. / Brady, R.L.
History
DepositionMar 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 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: Glyoxylate reductase/hydroxypyruvate reductase
B: Glyoxylate reductase/hydroxypyruvate reductase
C: Glyoxylate reductase/hydroxypyruvate reductase
D: Glyoxylate reductase/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,15215
Polymers143,4774
Non-polymers3,67411
Water11,007611
1
A: Glyoxylate reductase/hydroxypyruvate reductase
B: Glyoxylate reductase/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4326
Polymers71,7392
Non-polymers1,6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-61 kcal/mol
Surface area24820 Å2
MethodPISA
2
C: Glyoxylate reductase/hydroxypyruvate reductase
D: Glyoxylate reductase/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7209
Polymers71,7392
Non-polymers1,9817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-110 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.568, 66.877, 149.780
Angle α, β, γ (deg.)90.00, 98.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological unit is a dimer, 2 dimers are present in the asymmetric unit (A,B and C,D).

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Components

#1: Protein
Glyoxylate reductase/hydroxypyruvate reductase


Mass: 35869.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTrcHisB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ7, glyoxylate reductase (NADP+)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-DGY / (2R)-2,3-DIHYDROXYPROPANOIC ACID


Mass: 106.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.7 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 8000, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 69070 / % possible obs: 90.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.121 / Χ2: 1.059 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 72.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.275 / Num. unique obs: 5483 / Χ2: 0.577 / % possible all: 72.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
PHASERV. 1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GDH
Resolution: 2.2→46.2 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.866 / SU B: 13.529 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.282 3460 5 %RANDOM
Rwork0.201 ---
all0.205 ---
obs0.205 69056 90.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.362 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-1.68 Å2
2---1.72 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9859 0 231 611 10701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210275
X-RAY DIFFRACTIONr_angle_refined_deg1.8572.00813994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88851290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51323.632402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.406151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1061582
X-RAY DIFFRACTIONr_chiral_restr0.1270.21640
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027550
X-RAY DIFFRACTIONr_nbd_refined0.2250.24977
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2618
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.221
X-RAY DIFFRACTIONr_mcbond_it0.7061.56671
X-RAY DIFFRACTIONr_mcangle_it1.128210370
X-RAY DIFFRACTIONr_scbond_it2.03534088
X-RAY DIFFRACTIONr_scangle_it2.9324.53624
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 203 -
Rwork0.212 3530 -
obs-3733 65.65 %
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)
15.1620.1027-2.48724.16560.21554.44440.1429-0.95430.2970.5247-0.18510.3123-0.04450.33710.04220.01890.01920.03520.1709-0.00890.073617.38118.478113.6789
25.7005-0.5704-1.78934.2297-0.02371.9443-0.1308-0.4884-0.45270.15760.0634-0.0748-0.02490.41950.0674-0.0270.03180.03430.10680.0523-0.024624.04971.15448.3951
30.78530.4419-0.29113.8385-1.35721.3114-0.0137-0.0033-0.1416-0.02760.01560.20540.0703-0.077-0.0019-0.0508-0.0044-0.02180.0344-0.01420.10414.1637.3018-3.3926
42.661-0.0743-0.87450.68770.5211.00860.14340.1261-0.2532-0.17820.0498-0.04260.04830.044-0.19320.06170.00820.01270.0878-0.01570.027233.760132.1185-26.0884
51.396-0.0748-0.70982.0109-0.410.46090.02390.0734-0.0142-0.1343-0.0350.4512-0.1605-0.03490.01110.0253-0.0584-0.04070.1023-0.00530.13097.896522.5622-18.9114
60.09520.1216-0.766412.3641-3.86846.8509-0.01010.11550.2597-0.78670.18640.78430.3422-0.6211-0.17630.0075-0.0371-0.04670.24780.02770.11576.056923.2982-21.9518
71.8585-3.4615-2.22989.0970.41367.9522-0.27810.02760.2674-0.4470.23520.55920.6285-0.73440.04290.0602-0.1497-0.14260.2420.01670.21420.714418.7867-23.102
83.33570.65651.15992.3138-1.63741.9966-0.23790.2747-0.4341-0.31740.17260.0310.5206-0.3480.06530.1191-0.0770.01510.0317-0.0720.051413.830311.7277-26.5051
94.2407-0.40630.99882.4062-0.69441.9839-0.1790.1676-0.2382-0.32080.0348-0.17080.3450.1460.14420.12770.00620.0465-0.0276-0.01050.01724.932811.3247-21.9943
101.17040.1123-0.39810.6814-0.27230.5938-0.0681-0.14730.0291-0.01050.01030.2441-0.0415-0.05720.05770.01020.02890.05310.0940.00040.109311.583913.08893.1864
114.1386-0.47052.07742.7053-0.92971.97320.22540.5060.0804-0.1221-0.21830.1447-0.01370.2277-0.00710.03880.06690.0580.21020.0218-0.012131.288546.1664-45.616
122.7376-1.98841.43783.3427-2.08843.85470.05860.21870.340.02610.0758-0.16070.0314-0.1404-0.1344-0.01910.0380.09370.0751-0.0040.029440.206848.1978-37.5433
134.37376.68530.115914.8526-2.29251.3194-0.2126-0.05440.1890.6448-0.0935-0.0644-0.07880.22250.30620.08920.00780.07720.1694-0.01540.094341.599259.2789-33.7455
141.93430.8693-1.40423.0592-1.73732.59590.16930.07340.20240.03970.02410.0565-0.2562-0.0755-0.19340.04380.00750.04210.0217-0.00660.008826.829948.244-26.6862
150.8772-1.1562-0.19951.53890.1470.9392-0.0121-0.15310.0816-0.198-0.1821-0.101-0.07880.20460.19420.0445-0.0022-0.00250.12470.04150.074729.207817.0201-6.6544
161.1102-0.7264-0.05991.72380.38440.3184-0.0231-0.04670.18120.1205-0.08380.0215-0.0968-0.01040.10680.0343-0.01230.01430.0686-0.00750.112215.171241.8819-10.3665
176.9609-1.40741.1715.9781.33914.45110.1259-0.18460.21470.2458-0.2579-0.1028-0.2036-0.290.132-0.02660.00920.07620.0469-0.02870.091412.28949.939-8.9512
182.8508-0.4245-1.17683.81062.3491.74680.1934-0.21920.2653-0.03550.264-0.122-0.3881-0.1832-0.45740.081-0.01030.02780.0726-0.0280.130123.881946.2246-7.5704
192.509-0.7807-0.90221.38180.35352.11410.1035-0.25670.1704-0.01590.0723-0.03290.0310.1929-0.17580.0082-0.03130.00950.0867-0.05170.029334.597840.2439-8.1376
201.5937-0.90950.94831.3322-1.15241.12370.12590.17240.1628-0.2581-0.0779-0.01830.1543-0.0277-0.0480.05450.04340.02770.11330.03480.05323.799946.69-35.3319
213.56983.53080.31373.6001-0.38624.52330.33460.4775-0.48540.16280.1480.07040.2431-0.8245-0.48260.08640.01660.01840.1455-0.06480.0618-41.401322.161-55.3463
225.6682-0.6531-5.01751.3849-0.77795.84550.02420.5409-0.42610.05960.11820.04380.1112-0.5069-0.14240.1707-0.00520.04850.19120.00350.1105-46.185417.3065-53.4585
235.75720.0048-2.03780.2954-0.49615.7260.05150.31870.4864-0.16060.08840.4562-0.07750.0784-0.13990.13620.0287-0.0090.03170.0269-0.0131-34.463526.8433-62.4485
241.5966-2.7903-0.07694.89810.32641.7126-0.0050.0992-0.03960.11030.0644-0.1396-0.37960.0421-0.05940.12460.00340.01610.0478-0.00530.002-34.147930.2667-51.4586
250.6376-0.6384-0.51371.25140.53530.8569-0.0503-0.1-0.0050.16410.0548-0.1117-0.04220.1148-0.00450.0307-0.0205-0.00710.0952-0.00730.0213-15.06848.5721-53.7697
262.0401-2.5145-2.91433.52593.2294.4717-0.2235-0.3766-0.83030.5244-0.31640.66860.04520.14930.53990.1018-0.00780.01190.1298-0.03150.0887-16.33835.0528-41.8902
274.5627-0.08130.30723.71531.77751.9727-0.2247-0.8750.30130.34590.1301-0.261-0.05820.40560.09460.1309-0.0712-0.0790.3297-0.0529-0.1181-7.86577.2751-36.5449
281.5235-0.1325-1.51691.21551.13592.92580.2064-0.30720.36950.04730.0572-0.0849-0.31360.3104-0.26360.0374-0.0804-0.03670.1039-0.04420.0686-4.964215.3149-48.3484
291.9188-0.4574-0.42360.7190.41691.51430.0141-0.09460.17780.06660.0568-0.0658-0.19390.0786-0.07090.0724-0.01090.0229-0.00760.02030.0284-17.776715.1449-55.984
3010.0877-8.2744-2.354716.05882.2991.5992-0.8434-1.65452.47310.83120.6251-1.4929-0.03140.33210.21830.09710.0128-0.00040.09690.01090.0795-33.222418.9851-38.5798
3113.3977-7.92093.25445.7223-0.01713.84070.9470.5875-0.4248-0.093-0.57280.05430.80060.781-0.37420.03730.118-0.10160.0487-0.00750.070615.958-16.0564-62.88
322.14520.35790.68731.2675-1.04821.33970.56790.5651-0.3108-0.6933-0.30430.19291.01781.0854-0.26360.40510.4239-0.20490.2991-0.10610.070312.4918-22.3684-70.3212
332.21931.8190.22192.7269-1.62964.8208-0.19150.0043-0.1723-0.0505-0.0985-0.4330.82630.63550.290.07670.1993-0.11860.0334-0.02770.09443.8463-27.8147-61.4487
340.7199-0.2745-0.30060.6710.22111.190.0252-0.10010.033-0.0969-0.0501-0.0587-0.0781-0.13290.02490.04870.0161-0.00390.10140.01130.0116-17.56013.9068-61.3616
350.4988-0.129-0.50534.5268-1.05382.0305-0.2681-0.1051-0.04890.33160.0825-0.20310.29170.03050.18560.13890.02260.05130.0314-0.0162-0.0253-18.2955-11.7276-51.1008
361.58160.9552-0.58534.5565-0.91370.8659-0.1947-0.2051-0.1845-0.17920.02280.03550.3960.06820.17190.14450.01340.0680.05150.0407-0.0007-22.5416-18.3581-50.8184
372.89360.99221.3110.34030.43991.9622-0.25120.1127-0.69441.40960.2792-0.62660.42210.5445-0.0280.24040.08390.19880.1493-0.00720.1746-18.3973-23.5486-66.2226
382.6419-0.0106-1.61381.2788-0.48414.0281-0.25780.3172-0.0733-0.08640.12330.02640.5581-0.09030.13460.1326-0.0470.0405-0.007-0.0357-0.0351-18.9145-11.1936-70.0649
3911.9504-3.81025.69431.5295-1.95873.48290.1502-0.1303-0.6508-0.0351-0.0140.04430.27830.2514-0.13620.05260.09520.0230.19330.08120.08476.9812-14.8421-56.8683
407.4155-3.4702-9.1951.6244.30311.4015-0.37172.487-1.1971.7306-1.4382-2.44380.89560.13381.80990.2380.0501-0.02730.16280.00040.16377.3209-29.1313-52.946
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 218 - 23
22AA22 - 4324 - 45
33AA44 - 12246 - 124
44AA123 - 145125 - 147
55AA146 - 164148 - 166
66AA165 - 180167 - 182
77AA181 - 200183 - 202
88AA201 - 231203 - 233
99AA232 - 283234 - 285
1010AA284 - 322286 - 324
1111BB6 - 258 - 27
1212BB26 - 5628 - 58
1313BB57 - 6659 - 68
1414BB67 - 11969 - 121
1515BB120 - 143122 - 145
1616BB144 - 180146 - 182
1717BB181 - 197183 - 199
1818BB198 - 215200 - 217
1919BB216 - 284218 - 286
2020BB285 - 322287 - 324
2121CC5 - 117 - 13
2222CC12 - 2614 - 28
2323CC27 - 4329 - 45
2424CC44 - 7046 - 72
2525CC71 - 15373 - 155
2626CC154 - 166156 - 168
2727CC167 - 200169 - 202
2828CC201 - 240203 - 242
2929CC241 - 315243 - 317
3030CC316 - 321318 - 323
3131DD6 - 188 - 20
3232DD19 - 6921 - 71
3333DD70 - 10072 - 102
3434DD101 - 141103 - 143
3535DD142 - 167144 - 169
3636DD168 - 209170 - 211
3737DD210 - 224212 - 226
3838DD225 - 285227 - 287
3939DD286 - 312288 - 314
4040DD313 - 322315 - 324

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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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