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- PDB-2qf2: Rat cytosolic PEPCK in complex with oxaloacetic acid and GDP. -

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Basic information

Entry
Database: PDB / ID: 2qf2
TitleRat cytosolic PEPCK in complex with oxaloacetic acid and GDP.
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / PEPCK / phosphoenolpyruvate carboxykinase / kinase / OAA / GDP / gluconeogenesis
Function / homology
Function and homology information


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular hypotonic response / cellular response to fructose stimulus / cellular hypotonic salinity response / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / cellular hyperosmotic response / positive regulation of memory T cell differentiation / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to lipid / response to starvation / cellular response to glucagon stimulus / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to nutrient levels / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to bacterium / response to insulin / lipid metabolic process / cellular response to insulin stimulus / GDP binding / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / manganese ion binding / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / cytosol / cytoplasm
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / OXALOACETATE ION / PYRUVIC ACID / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSullivan, S.M. / Holyoak, T.
CitationJournal: Biochemistry / Year: 2007
Title: Structures of rat cytosolic PEPCK: insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid.
Authors: Sullivan, S.M. / Holyoak, T.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
B: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,48618
Polymers139,2882
Non-polymers2,19816
Water21,7801209
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A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,99210
Polymers69,6441
Non-polymers1,3489
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4948
Polymers69,6441
Non-polymers8507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.506, 119.112, 86.710
Angle α, β, γ (deg.)90.00, 107.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoenolpyruvate carboxykinase, cytosolic [GTP] / / Phosphoenolpyruvate carboxylase / PEPCK-C


Mass: 69643.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: PGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 6 types, 1225 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1209 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 3350, 0.1M HEPES pH 7.4, 10 mM MnCl2, 10 mM GDP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2006 / Details: Bent conical Si-mirror (Rh coated)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 142474 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.693 / % possible all: 80.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QEW

2qew


Resolution: 1.65→33.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.834 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23762 7148 5 %RANDOM
Rwork0.20427 ---
obs0.20597 135193 96.45 %-
all-142341 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.121 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9584 0 123 1209 10916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.97814366
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52451378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16424.204471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.665151873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9031566
X-RAY DIFFRACTIONr_chiral_restr0.0840.21504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.25203
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27107
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.21079
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.290
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4011.56357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.724210330
X-RAY DIFFRACTIONr_scbond_it1.14634380
X-RAY DIFFRACTIONr_scangle_it1.864.53963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 443 -
Rwork0.288 8018 -
obs--77.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.25750.6596-0.02049.74581.37914.1737-0.26640.0943-0.1325-0.23240.2895-0.96530.01650.6996-0.0231-0.06690.0110.02730.14360.02510.156751.306415.1093-5.5926
21.0736-0.0885-0.48840.95540.55141.26570.04430.02970.1232-0.0179-0.14320.0484-0.2833-0.05230.09890.06360.0115-0.02520.0342-0.01150.071632.078721.29822.3424
30.29430.47450.1891.96020.16680.8452-0.0590.04340.011-0.0935-0.0497-0.0080.0697-0.00580.10870.0530.0120.03440.0689-0.00350.045733.94861.1749-8.4127
40.51260.16580.4511.18990.52711.87070.01470.0420.05390.0197-0.17050.06640.1178-0.00430.15580.01710.0049-0.00690.07160.00460.071435.012510.8484-4.465
50.49550.0321-0.12140.387-0.61560.9895-0.0108-0.054-0.0487-0.0327-0.0087-0.0277-0.16070.05530.01950.1342-0.03950.00210.0781-0.01770.02927.53-4.043112.3342
60.5839-0.72490.25021.5347-0.40210.3891-0.00230.0132-0.05820.309-0.08780.2056-0.1102-0.00320.09010.0483-0.02630.04340.0773-0.0720.09820.498911.177414.6469
70.42730.5271-0.13150.9697-0.31790.17320.0215-0.05850.0187-0.1308-0.02270.0699-0.024-0.06130.00120.06920.0158-0.0010.0901-0.04040.048320.0179-3.64457.3804
80.8802-0.27120.53561.55070.87782.87430.0121-0.1651-0.12-0.032-0.1904-0.0304-0.1163-0.37340.1783-0.02150.0085-0.0210.10250.00080.05515.6201-15.183418.7583
98.0582.1934-2.65640.6534-1.29026.58760.6751-0.18390.19010.8496-0.47670.77270.9066-1.1767-0.19840.2106-0.0033-0.04590.2026-0.050.18354.2505-12.580423.9842
102.04160.725-0.471.6785-0.29981.9731-0.12480.0319-0.216-0.35550.04160.11460.0709-0.2450.08320.0664-0.012-0.02220.0509-0.03940.068112.8902-24.14070.1027
111.2921-0.19020.72034.7255-0.14773.06750.01910.1031-0.0688-0.17410.048-0.5332-0.0240.2851-0.0671-0.0717-0.0109-0.00560.12320.01560.121131.402715.188-48.4672
120.98820.5076-0.16782.02370.40040.78930.0505-0.00350.31140.2044-0.1570.3896-0.07210.03330.10640.0113-0.0114-0.01060.0264-0.03780.148211.488921.8038-38.4583
130.44520.77730.06491.75670.26890.4877-0.00340.03930.04560.0003-0.03090.0813-0.0086-0.0070.0344-0.01090.0059-0.05820.10660.00470.052815.04115.9085-48.3444
140.30180.567-0.15751.5708-0.56730.22790.13190.00450.07010.3012-0.1410.0005-0.10910.10020.00910.0845-0.0279-0.05340.1276-0.00750.02811.7975-3.1697-35.9868
150.71370.4803-0.24992.0739-0.34980.26430.2873-0.1330.19920.6477-0.2540.2355-0.10210.1625-0.03330.237-0.10140.06870.0686-0.06980.00675.3540.0804-24.4597
161.4721-0.98051.76771.9311-2.78927.65230.1272-0.39430.19860.550.31180.59710.0957-1.2865-0.439-0.0514-0.07760.19350.2405-0.08690.3701-5.324420.6404-28.8889
170.59780.795-0.11641.1138-0.18190.03570.11-0.02430.11530.2807-0.05490.31040.0040.0269-0.05510.0765-0.00710.02320.1034-0.02360.08970.7443-3.7927-34.304
181.09250.11670.31111.2829-0.27881.43090.1716-0.0583-0.03020.5138-0.11290.2028-0.1066-0.0799-0.05870.1554-0.03210.06770.0375-0.01170.0155-4.6891-14.9429-22.7922
190.62560.0696-0.22211.047-0.23161.98070.0590.1148-0.07920.12970.00280.2587-0.0832-0.2477-0.06180.0136-0.0082-0.00320.06170.0180.1098-9.2552-18.2928-35.102
2012.26060.6423-3.1512.93130.03772.825-0.07360.2811-0.1475-0.17470.00090.33690.0616-0.09770.07260.01480.0038-0.06850.0639-0.00740.0951-6.6876-29.2533-38.1766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 3212 - 34
2X-RAY DIFFRACTION2AA33 - 8835 - 90
3X-RAY DIFFRACTION3AA89 - 16291 - 164
4X-RAY DIFFRACTION4AA163 - 232165 - 234
5X-RAY DIFFRACTION5AA233 - 317235 - 319
6X-RAY DIFFRACTION6AA318 - 386320 - 388
7X-RAY DIFFRACTION7AA387 - 499389 - 501
8X-RAY DIFFRACTION8AA500 - 562502 - 564
9X-RAY DIFFRACTION9AA563 - 579565 - 581
10X-RAY DIFFRACTION10AA580 - 622582 - 624
11X-RAY DIFFRACTION11BB9 - 3811 - 40
12X-RAY DIFFRACTION12BB39 - 8941 - 91
13X-RAY DIFFRACTION13BB90 - 22392 - 225
14X-RAY DIFFRACTION14BB224 - 286226 - 288
15X-RAY DIFFRACTION15BB287 - 352289 - 354
16X-RAY DIFFRACTION16BB353 - 385355 - 387
17X-RAY DIFFRACTION17BB386 - 500388 - 502
18X-RAY DIFFRACTION18BB501 - 562503 - 564
19X-RAY DIFFRACTION19BB563 - 608565 - 610
20X-RAY DIFFRACTION20BB609 - 622611 - 624

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Yorodumi

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  • 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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