[English] 日本語
Yorodumi
- PDB-5t1m: Cetuximab Fab in complex with CQYDLSTRRLKC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t1m
TitleCetuximab Fab in complex with CQYDLSTRRLKC
Components
  • (CETUXIMAB FAB ...) x 2
  • CYCLIC PEPTIDE CQYDLSTRRLKC
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CETUXIMAB FAB LIGHT CHAIN
B: CETUXIMAB FAB HEAVY CHAIN
C: CETUXIMAB FAB LIGHT CHAIN
D: CETUXIMAB FAB HEAVY CHAIN
E: CYCLIC PEPTIDE CQYDLSTRRLKC
F: CYCLIC PEPTIDE CQYDLSTRRLKC
H: CYCLIC PEPTIDE CQYDLSTRRLKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,47115
Polymers98,4597
Non-polymers1,0128
Water8,557475
1
A: CETUXIMAB FAB LIGHT CHAIN
B: CETUXIMAB FAB HEAVY CHAIN
E: CYCLIC PEPTIDE CQYDLSTRRLKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9917
Polymers48,4853
Non-polymers5064
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-43 kcal/mol
Surface area18940 Å2
MethodPISA
2
C: CETUXIMAB FAB LIGHT CHAIN
D: CETUXIMAB FAB HEAVY CHAIN
F: CYCLIC PEPTIDE CQYDLSTRRLKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9917
Polymers48,4853
Non-polymers5064
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-43 kcal/mol
Surface area18990 Å2
MethodPISA
3
H: CYCLIC PEPTIDE CQYDLSTRRLKC


Theoretical massNumber of molelcules
Total (without water)1,4891
Polymers1,4891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.200, 82.500, 212.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 4 molecules ACBD

#1: Antibody CETUXIMAB FAB LIGHT CHAIN


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: unidentified (others)
#2: Antibody CETUXIMAB FAB HEAVY CHAIN


Mass: 23708.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: unidentified (others)

-
Protein/peptide / Sugars , 2 types, 5 molecules EFH

#3: Protein/peptide CYCLIC PEPTIDE CQYDLSTRRLKC


Mass: 1488.756 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 481 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M CITRIC ACID, 0.1 M SODIUM HYDROGEN PHOSPHATE, 0.4 M POTASSIUM HYDROGEN PHOSPHATE, 1.6 M SODIUM DIHYDROGEN PHOSPHATE, PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 2011
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.53→32.99 Å / Num. obs: 37657 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.7
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.21 / % possible all: 91.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1


Resolution: 2.53→32.99 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.216 1883 5 %
Rwork0.153 --
obs0.156 37649 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.53→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6869 0 58 475 7402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077143
X-RAY DIFFRACTIONf_angle_d1.1449725
X-RAY DIFFRACTIONf_dihedral_angle_d13.1092566
X-RAY DIFFRACTIONf_chiral_restr0.0731099
X-RAY DIFFRACTIONf_plane_restr0.0051242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.59840.34081330.20912535X-RAY DIFFRACTION92
2.5984-2.67480.27431430.18972719X-RAY DIFFRACTION97
2.6748-2.76110.25561420.18442690X-RAY DIFFRACTION97
2.7611-2.85980.28461410.18292689X-RAY DIFFRACTION98
2.8598-2.97420.28261440.1862730X-RAY DIFFRACTION98
2.9742-3.10940.2491440.17932732X-RAY DIFFRACTION98
3.1094-3.27320.23861440.17422741X-RAY DIFFRACTION98
3.2732-3.47810.23321440.1572734X-RAY DIFFRACTION98
3.4781-3.74630.18011460.1382779X-RAY DIFFRACTION98
3.7463-4.12270.1861460.12662764X-RAY DIFFRACTION98
4.1227-4.71780.16411470.10772805X-RAY DIFFRACTION99
4.7178-5.93820.17321510.12212861X-RAY DIFFRACTION99
5.9382-32.99140.19981580.17442987X-RAY DIFFRACTION99
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)
13.00772.0789-1.00516.0191-3.68496.09230.08650.09920.00570.49460.3735-0.0072-1.0118-0.3166-0.4880.31250.08550.08880.2701-0.01360.208519.31-23.5611-18.8092
22.29190.64760.66813.4-1.23924.11170.1678-0.26410.31790.26870.0668-0.0663-0.4893-0.0277-0.22620.2526-0.0220.05030.2239-0.07010.185128.9194-27.1214-12.8749
33.11522.4675-1.69315.21240.11989.0883-0.416-0.2254-0.06260.01890.111-0.1018-1.64080.2262-0.27250.47680.07750.07130.2082-0.05340.239928.0408-19.1461-19.8939
41.1344-0.62890.8781.28640.26891.29690.1934-0.34280.2560.51380.27620.5765-0.4559-0.5155-0.37750.1992-0.00740.08240.2472-0.04550.214423.2216-34.9959-13.2109
51.24251.9928-2.77483.3853-4.82836.72360.24490.07190.49410.56260.350.3549-0.44630.0265-0.47920.3210.01530.08880.1664-0.01580.272524.8471-18.3487-34.8163
63.5729-1.1705-0.06654.62470.27232.03410.27720.4752-0.3593-0.5974-0.0518-0.2590.37160.265-0.2010.28150.11490.0620.2489-0.02660.191334.6702-36.7178-57.7245
71.12571.83670.88585.62585.16516.23440.04690.09460.07470.4903-0.17980.26780.3104-0.41650.10220.0849-0.00790.02880.17310.0030.22624.7231-27.224-50.505
82.9090.08922.50980.52681.36825.3248-0.13370.10760.2339-0.1214-0.20410.1598-0.144-0.20690.41470.1479-0.0317-0.02110.2534-0.0120.295319.9456-33.4173-55.4268
92.47890.64330.7882.67531.28853.5813-0.02710.33240.0829-0.2485-0.02630.1635-0.06030.15610.00820.09270.03520.00970.15690.01810.186826.7452-28.2912-54.68
104.72131.13183.40763.31273.07527.6667-0.15940.3419-0.01190.05440.2220.20290.67290.8882-0.0720.19360.02340.00070.24320.0180.165435.4385-50.1189-25.0619
111.5182-0.11940.35941.7686-0.46614.43050.0317-0.1262-0.10390.02570.03780.02960.370.0999-0.07340.1965-0.01670.0030.1479-0.01810.131532.5838-46.93-16.062
123.25170.6887-0.05791.56291.70153.76520.0958-0.08440.5363-1.493-0.15580.76850.11820.2866-0.05910.13010.0660.03610.163-0.06170.216437.8821-33.9572-52.3676
131.85160.7925-1.4922.5512-1.10631.6138-0.1024-0.050.0135-0.01320.0268-0.13310.17730.01960.07260.11030.014-0.02830.1134-0.02310.157535.4665-36.7215-43.9083
143.79732.9309-1.60346.4593-3.83554.2346-0.24230.1707-0.1312-0.02570.2211-0.2780.07420.06270.05610.10960.05140.00520.2095-0.00030.224945.2426-37.7361-47.6272
155.03391.71920.56876.19241.8625.04290.34480.0257-0.1677-0.18480.0294-0.66360.7940.4301-0.34160.34360.079-0.09140.24710.03370.179211.9363-16.7077-17.7089
161.81980.2824-0.43393.4962-0.03224.976-0.0863-0.1703-0.15620.24050.17550.05410.6723-0.2494-0.09520.21410.0295-0.00130.18130.04010.16313.1188-13.9996-11.6136
170.10280.14410.02130.41340.31532.73570.0248-0.1182-0.14620.19420.1719-0.00940.5030.2429-0.18720.24150.0812-0.04570.19270.00860.21665.6784-13.6756-21.0628
180.62190.2842-1.17015.3467-2.77063.3999-0.01890.1232-0.0933-0.19580.0290.070.07860.0263-0.00260.0889-0.048-0.05630.1212-0.03210.13822.9981-5.8355-51.6746
190.6211.2205-0.81762.055-2.19183.0139-0.12310.0824-0.23030.20110.1264-0.1933-0.1517-0.09420.0070.08980.01150.01160.2315-0.03680.20966.5511-9.5075-44.7844
200.9261-0.6128-0.1446.1893-2.87414.4013-0.04510.2096-0.1155-0.55370.02150.03320.2816-0.00340.01410.0981-0.07430.02610.1896-0.05620.15856.2159-6.5688-58.1499
213.95364.6274-5.70927.9983-5.13959.2901-0.28370.2416-0.0422-0.45490.2201-0.0134-0.7056-0.5582-0.07220.29260.0955-0.01490.27720.01490.2094-3.17210.8921-21.8877
222.48190.4348-0.5882.89570.80113.2160.0653-0.13580.05640.0947-0.00540.0369-0.4728-0.3305-0.07690.22960.0562-0.0010.21550.01220.1104-0.82655.3856-10.1939
232.74980.8289-1.57562.2619-1.50324.32520.0274-0.10090.3268-0.00520.06610.0909-0.75450.1107-0.09890.37510.0208-0.02820.26-0.03490.152-0.055410.1332-14.0032
240.86030.6630.73610.79230.37294.1577-0.03150.0420.07640.10940.056-0.0202-0.1987-0.1469-0.06420.13110.06350.05090.1362-0.00020.1554-0.43373.1464-17.6275
254.06590.28130.40681.2353-1.63424.0561-0.35660.2199-0.2731-1.06020.4624-0.06-0.323-0.2375-0.12910.0297-0.00730.01710.168-0.01180.1048-6.1668-1.954-49.6752
264.11962.83460.68894.86111.68713.58550.0507-0.1016-0.13360.2080.16330.2274-0.3168-0.2403-0.16760.1270.0443-0.0040.13410.05560.2028-5.79122.292-40.0141
273.82452.40851.46115.0340.66862.31760.13960.0712-0.1270.0920.0432-0.0216-0.0278-0.0496-0.17630.11020.00570.02350.1125-0.00690.1245-2.8819-3.9165-43.589
285.0721.65072.8625.68691.82288.18410.3407-0.3419-0.2261-0.1547-0.26980.9319-0.1112-0.9708-0.02080.12310.05190.01640.31010.04960.3344-15.7158-3.0024-45.4508
296.41292.22640.49576.09543.4555.4729-0.3493-0.23180.3012-0.4279-0.16760.5283-0.5993-0.45350.42990.10170.02670.00360.21710.02890.1871-11.04475.096-44.5619
307.6505-1.4343-4.68175.0482.58176.23720.05410.34940.1661-0.2121-0.22070.3614-0.0491-0.88720.12490.1152-0.0118-0.00950.3504-0.01430.200423.3947-34.986-30.7823
312.8835-4.02331.25978.6374-1.40927.07420.02150.0527-0.0805-0.3471-0.0374-0.32180.09890.8743-0.01150.13820.05310.02680.3158-0.00880.15498.2973-4.2143-28.8049
322.55970.5443-3.45774.87750.13185.4358-0.6694-0.6119-1.29170.8062-0.2999-1.39721.53680.97570.92091.21050.1742-0.10350.670.20250.707445.3125-18.2657-61.9508
331.99943.95670.92071.3507-0.13722.9777-0.7620.6567-1.2065-1.51281.2937-2.48480.10470.3256-0.4121.40590.1538-0.04340.5995-0.62650.827815.418-49.5959-22.5306
341.99961.32770.96421.6689-2.94746.0592-1.63652.73562.9284-4.40952.42611.45851.0974-1.7446-0.52080.7553-0.60860.0531.08520.19660.70416.51548.5937-19.6409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:25 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 26:69 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 70:83 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 84:101 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 102:113 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 114:128 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 129:150 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 151:163 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 164:213 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 1:21 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 22:121 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 122:142 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 143:192 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 193:220 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 1:25 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 26:75 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 76:113 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 114:150 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 151:174 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 175:213 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 1:21 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 22:61 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 62:101 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 102:121 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 122:145 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 146:165 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 166:195 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 196:205 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 206:220 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 1:12 )
31X-RAY DIFFRACTION31CHAIN F AND (RESID 1:12 )
32X-RAY DIFFRACTION32CHAIN H AND (RESID 1:12 )
33X-RAY DIFFRACTION33CHAIN B AND (RESID 301:301)
34X-RAY DIFFRACTION34CHAIN D AND (RESID 301:301)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more