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Basic information

Entry
Database: PDB / ID: 4elg
TitleStructure-activity relationship guides enantiomeric preference among potent inhibitors of B. anthracis dihydrofolate reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / dihydrofolate reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-52I / Chem-52J / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsBourne, C.R. / Barrow, W.W.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase.
Authors: Bourne, C.R. / Wakeham, N. / Nammalwar, B. / Tseitin, V. / Bourne, P.C. / Barrow, E.W. / Mylvaganam, S. / Ramnarayan, K. / Bunce, R.A. / Berlin, K.D. / Barrow, W.W.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
F: Dihydrofolate reductase
G: Dihydrofolate reductase
H: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,53434
Polymers156,9248
Non-polymers5,61026
Water22,6631258
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1924
Polymers19,6151
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6925
Polymers19,6151
Non-polymers1,0774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1924
Polymers19,6151
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1924
Polymers19,6151
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1924
Polymers19,6151
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1924
Polymers19,6151
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6925
Polymers19,6151
Non-polymers1,0774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1924
Polymers19,6151
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.151, 135.655, 168.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Dihydrofolate reductase /


Mass: 19615.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: A thrombin cut site was engineered between the C-terminus and the 6 x His tag
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2083, BA_2237, dfrA, DHFR, GBAA_2237 / Plasmid: pCR-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81R22, dihydrofolate reductase

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Non-polymers , 5 types, 1284 molecules

#2: Chemical
ChemComp-52J / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(2-methylpropyl)phthalazin-2(1H)-yl]prop-2-en-1-one / (S,E)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-isobutylphthalazin-2(1H)-yl)prop-2-en-1-one


Mass: 500.592 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C28H32N6O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-52I / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1R)-1-(2-methylpropyl)phthalazin-2(1H)-yl]prop-2 -en-1-one / (R,E)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-isobutylphthalazin-2(1H)-yl)prop-2-en-1-one


Mass: 500.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H32N6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1258 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 16-22% PEG 3350, 0.2M CaCl2, 0.1M MES, +/- 3% glycerol , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 87128 / % possible obs: 95.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FL8
Resolution: 2.101→48 Å / SU ML: 0.73 / σ(F): 1.34 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 3842 2.29 %
Rwork0.1935 --
obs0.1949 86863 95.39 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.182 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.749 Å20 Å2-0 Å2
2--6.1969 Å20 Å2
3----8.946 Å2
Refinement stepCycle: LAST / Resolution: 2.101→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11034 0 386 1258 12678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111782
X-RAY DIFFRACTIONf_angle_d1.12415998
X-RAY DIFFRACTIONf_dihedral_angle_d17.5444451
X-RAY DIFFRACTIONf_chiral_restr0.0721602
X-RAY DIFFRACTIONf_plane_restr0.0052023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1014-2.1280.381150.28245049X-RAY DIFFRACTION79
2.128-2.1560.4021380.30245786X-RAY DIFFRACTION91
2.156-2.18560.38241330.26615824X-RAY DIFFRACTION91
2.1856-2.21680.31531360.25065749X-RAY DIFFRACTION91
2.2168-2.24990.30241380.22815841X-RAY DIFFRACTION92
2.2499-2.2850.30971410.24125994X-RAY DIFFRACTION94
2.285-2.32250.31460.2216020X-RAY DIFFRACTION94
2.3225-2.36250.31751460.21356046X-RAY DIFFRACTION95
2.3625-2.40550.30621450.21486107X-RAY DIFFRACTION96
2.4055-2.45180.29011430.21656087X-RAY DIFFRACTION96
2.4518-2.50180.32751420.22086097X-RAY DIFFRACTION96
2.5018-2.55620.30951420.21236140X-RAY DIFFRACTION96
2.5562-2.61570.27271430.2086140X-RAY DIFFRACTION97
2.6157-2.68110.28021380.20626127X-RAY DIFFRACTION97
2.6811-2.75350.34051470.21556294X-RAY DIFFRACTION98
2.7535-2.83460.28181490.20636282X-RAY DIFFRACTION99
2.8346-2.9260.26891470.19786238X-RAY DIFFRACTION99
2.926-3.03060.31211470.20336239X-RAY DIFFRACTION98
3.0306-3.15190.2441500.20446299X-RAY DIFFRACTION98
3.1519-3.29530.25581480.18986185X-RAY DIFFRACTION98
3.2953-3.4690.22581500.19736244X-RAY DIFFRACTION98
3.469-3.68630.25761450.19526246X-RAY DIFFRACTION98
3.6863-3.97080.23111430.17216226X-RAY DIFFRACTION98
3.9708-4.37020.22891420.1466212X-RAY DIFFRACTION98
4.3702-5.0020.15531410.12426151X-RAY DIFFRACTION97
5.002-6.29970.19171460.16946142X-RAY DIFFRACTION97
6.2997-48.08780.23741410.21275899X-RAY DIFFRACTION93
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)
10.49140.1376-0.76732.7902-1.65725.80630.0275-0.00110.0930.0711-0.0246-0.0141-0.33950.34930.00260.1449-0.0217-0.02070.2299-0.02940.222616.5884-30.471-4.6193
20.6849-0.34430.21322.4083-0.66373.41850.02390.06270.05-0.3301-0.0284-0.0278-0.21260.02170.00450.1313-0.0003-0.00860.19630.00120.206514.5436-33.0564-10.0045
36.8389.21716.81332.01698.15517.84090.039-0.77020.12431.2133-0.42040.680.0476-0.53310.34480.51790.1054-0.18080.3778-0.12880.46354.5866-52.6386-22.623
40.1208-0.57110.53492.3092-1.83633.4633-0.02430.0705-0.1086-0.3917-0.0449-0.26060.30870.42770.0510.18420.00510.04710.2613-0.01690.235614.1145-5.00075.5567
50.70340.3398-0.13771.4945-1.59773.5115-0.00330.07220.02420.00170.02740.02370.0907-0.1517-0.02030.11070.00830.02040.2033-0.0070.205810.5280.11549.1422
62.0022-6.8842-9.77987.59125.67642.0052-0.26310.5919-2.5388-0.20680.2235-0.22941.93950.78070.15350.57780.16770.0670.5249-0.27140.84393.026120.365723.9812
72.0182-0.39230.79490.15040.35153.75610.0268-0.20530.01660.24320.07070.03130.037-0.171-0.08920.33560.05020.00320.157-0.00190.207116.1499-35.1436.7248
80.96140.33831.12731.04930.57593.57770.0117-0.0227-0.12140.28970.04610.03280.2662-0.0911-0.05270.24950.03560.02020.1428-0.01460.200719.3253-38.744331.8828
92.00875.02380.13632.25122.54581.9999-0.3611-0.2579-0.68440.39430.10640.87910.65480.01230.21780.8128-0.07260.18870.3033-0.05310.478841.8435-48.535318.2473
106.0858-1.1179-3.8981.6790.43136.5240.2179-0.07520.56410.15920.0375-0.0633-0.9957-0.5036-0.19940.34760.0658-0.02850.1993-0.00890.26686.820234.6631-4.1444
110.5687-0.83350.11031.8783-1.29014.6014-0.0364-0.07890.14060.0765-0.0693-0.0974-0.73440.24680.09890.2515-0.0382-0.04380.2149-0.01040.204312.54134.2358-9.1934
122.0005-5.69361.99969.5929-2.79282.0024-0.8728-0.40362.75650.57770.22440.1743-0.7015-1.05920.62640.51040.2294-0.06651.1169-0.37980.91272.681311.2689-25.1589
131.33020.03751.07241.2843-0.28642.7393-0.0254-0.140.19030.0475-0.06380.1389-0.7199-0.59590.06950.45950.11080.00640.2819-0.02040.212311.442431.695736.6298
141.37990.46260.35871.07650.73323.7252-0.02880.1960.01850.0077-0.02070.061-0.4433-0.28610.04250.35930.0499-0.04420.1666-0.0050.198315.64727.893632.2089
153.96130.3667-1.5711.9239-4.28019.6775-0.51320.831-0.84670.3868-1.1982.42940.3878-2.18441.64520.6751-0.17740.3230.5435-0.3070.86637.170920.90717.7643
160.3103-0.50290.6062.6435-0.51492.5544-0.0958-0.27540.00590.15750.19760.30680.1742-0.5678-0.11920.1426-0.03090.01970.4484-0.04210.2518-18.2448-7.743240.9666
171.08120.37221.34630.7244-0.04683.1885-0.0675-0.15030.071-0.0181-0.020.1198-0.0839-0.37450.08250.13850.01390.01910.2882-0.07010.2099-18.559-4.042333.4857
182.0274-3.5995-7.17045.35136.2492.0182-0.3757-0.4163-0.42120.8288-0.25261.28660.3097-1.01510.55820.32660.02010.04190.5188-0.06290.44273.2717-13.957819.1672
190.9821-0.49760.24721.4985-0.73153.8875-0.08610.1560.21830.1797-0.0668-0.1232-0.38170.24590.15990.1663-0.0496-0.05120.2389-0.01390.2577-19.27863.2363-4.0745
200.6814-0.70910.77360.9866-0.73573.9291-0.04670.06780.0632-0.0285-0.1516-0.0107-0.2965-0.03360.18720.126-0.0462-0.03210.2326-0.00380.2142-22.5386-0.4164-8.9716
210.8133-2.01650.67432.01449.86622.00980.3058-0.22910.74560.1502-0.3422-0.0471-0.1072-0.93940.02640.4965-0.0888-0.02490.484-0.10130.3598-28.6456-22.0558-22.609
222.2020.08321.0971.0332-0.49375.5637-0.23310.01030.07650.19630.0077-0.4466-0.5450.94860.19620.231-0.0487-0.05970.31810.02650.287921.0488-1.86447.137
231.9278-0.77560.94992.3406-0.90835.2076-0.2135-0.40270.07110.44210.0452-0.1968-0.19530.24180.1280.19640.0199-0.01280.2523-0.00280.204616.0559-5.087651.2724
242.00637.8838-5.74292.0015-7.90972.0074-0.35430.3484-0.4675-0.93930.3735-1.81090.96491.56630.08610.59120.05180.25070.63750.10310.5745-3.6748-13.171567.6958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:55)
2X-RAY DIFFRACTION2(chain A and resid 56:159)
3X-RAY DIFFRACTION3(chain A and resid 160:166)
4X-RAY DIFFRACTION4(chain B and resid 1:65)
5X-RAY DIFFRACTION5(chain B and resid 66:161)
6X-RAY DIFFRACTION6(chain B and resid 162:166)
7X-RAY DIFFRACTION7(chain C and resid 1:59)
8X-RAY DIFFRACTION8(chain C and resid 60:161)
9X-RAY DIFFRACTION9(chain C and resid 162:166)
10X-RAY DIFFRACTION10(chain D and resid 1:23)
11X-RAY DIFFRACTION11(chain D and resid 24:161)
12X-RAY DIFFRACTION12(chain D and resid 162:166)
13X-RAY DIFFRACTION13(chain E and resid 1:62)
14X-RAY DIFFRACTION14(chain E and resid 63:161)
15X-RAY DIFFRACTION15(chain E and resid 162:166)
16X-RAY DIFFRACTION16(chain F and resid 1:29)
17X-RAY DIFFRACTION17(chain F and resid 30:160)
18X-RAY DIFFRACTION18(chain F and resid 161:166)
19X-RAY DIFFRACTION19(chain G and resid 1:60)
20X-RAY DIFFRACTION20(chain G and resid 61:160)
21X-RAY DIFFRACTION21(chain G and resid 161:166)
22X-RAY DIFFRACTION22(chain H and resid 1:65)
23X-RAY DIFFRACTION23(chain H and resid 66:161)
24X-RAY DIFFRACTION24(chain H and resid 162:166)

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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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