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- PDB-9cjq: X-ray crystal structure of SARS-CoV-2 main protease quadruple mut... -

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Basic information

Entry
Database: PDB / ID: 9cjq
TitleX-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir
Componentsmain protease
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex / SARS2
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / host cell endosome / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / lyase activity / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / copper ion binding / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / : / : / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Chem-7YY / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsEsler, M.A. / Shi, K. / Harris, R.S. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA214279 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI064064 United States
CitationJournal: Mbio / Year: 2025
Title: Structural basis for varying drug resistance of SARS-CoV-2 M pro E166 variants.
Authors: Esler, M.A. / Shi, K. / Rollie, J.A. / Delgado, R. / Vishwakarma, J. / Dabrowska, A. / Prahlad, J. / Moghadasi, S.A. / Harris, R.S. / Aihara, H.
History
DepositionJul 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: main protease
B: main protease
C: main protease
D: main protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,90210
Polymers135,6514
Non-polymers2,2526
Water3,153175
1
A: main protease
B: main protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9515
Polymers67,8252
Non-polymers1,1263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-12 kcal/mol
Surface area24890 Å2
MethodPISA
2
C: main protease
D: main protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9515
Polymers67,8252
Non-polymers1,1263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-13 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.022, 106.994, 116.522
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
main protease


Mass: 33912.711 Da / Num. of mol.: 4 / Fragment: UNP residues 3264-3570 / Mutation: T21I, L50F, S144A, E166V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTD1
#2: Chemical
ChemComp-7YY / 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione


Mass: 531.878 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H17ClF3N9O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antivirus, protease inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Data were collected for crystals of robot tray J000317: 0.05 M HEPES sodium, pH 7.0, 1% w/v Tryptone, 12% w/v PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.24→78.4 Å / Num. obs: 34334 / % possible obs: 90.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.33 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.067 / Rrim(I) all: 0.134 / Rsym value: 0.116 / Net I/σ(I): 5.8
Reflection shellResolution: 2.24→2.46 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1717 / CC1/2: 0.663 / Rpim(I) all: 0.5 / Rrim(I) all: 0.911 / Rsym value: 0.672

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→78.33 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1677 4.92 %
Rwork0.2212 --
obs0.223 34092 64.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→78.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9391 0 119 175 9685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d13.893438
X-RAY DIFFRACTIONf_chiral_restr0.0451467
X-RAY DIFFRACTIONf_plane_restr0.0081713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.264420.32167X-RAY DIFFRACTION2
2.3-2.380.4204300.3307544X-RAY DIFFRACTION13
2.38-2.460.3826640.3191093X-RAY DIFFRACTION27
2.46-2.560.3061000.30871712X-RAY DIFFRACTION42
2.56-2.680.32931250.29572272X-RAY DIFFRACTION55
2.68-2.820.33071620.28852766X-RAY DIFFRACTION66
2.82-2.990.31851640.27563430X-RAY DIFFRACTION82
2.99-3.220.29682300.25784091X-RAY DIFFRACTION99
3.23-3.550.25131860.22094148X-RAY DIFFRACTION99
3.55-4.060.24612070.19744141X-RAY DIFFRACTION99
4.06-5.120.20921960.17064118X-RAY DIFFRACTION98
5.12-78.330.20972110.19394033X-RAY DIFFRACTION95
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)
17.749-3.08795.46972.7839-1.99525.0811-0.2533-0.25430.29130.30180.2433-0.017-0.3184-0.2640.15230.50520.0925-0.15010.54740.07640.4708-8.227735.3799-10.3262
21.1320.2674-0.48556.06760.87720.3716-0.1549-0.1180.3047-0.1507-0.10320.4237-0.338-0.32910.17090.61510.1438-0.21520.5640.03170.4887-17.274141.0223-19.0621
33.4659-1.9437-0.69493.8599-0.90562.38920.18230.14450.0416-0.098-0.0579-0.29470.146-0.2181-0.14520.51940.045-0.19720.46820.01770.4635-4.784627.2413-13.1175
42.9215-0.2933-1.08923.52190.88641.4624-0.078-0.3088-1.11270.28890.26310.10080.00570.2404-0.04440.52190.0617-0.09240.52270.02180.4234.591811.9106-12.7536
53.896-1.6958-1.25494.731.11435.2743-0.1567-0.3663-0.2579-0.0840.05470.05380.09790.20690.06090.49590.0279-0.25320.62480.0810.612611.919710.1456-11.2332
62.14520.2835-0.20942.4416-0.32023.0514-0.0083-0.0450.1870.03650.0626-0.1042-0.40990.2685-0.05150.5028-0.0374-0.17340.4327-0.0020.47379.791735.810714.0365
79.11120.3525-1.23263.33080.26673.64260.12190.36471.00120.0142-0.04210.18760.28360.0748-0.02620.4961-0.0004-0.15620.3985-0.00810.31292.842331.16238.9597
80.78250.9586-0.64072.23480.46812.00370.0788-0.2311-0.21650.27250.0314-0.06290.26650.354-0.17040.498-0.0154-0.26390.47050.06290.48028.754223.661118.249
92.24470.5068-1.39686.0927-0.47623.4256-0.15560.5866-0.70710.08840.14240.12010.1041-0.5836-0.02370.5098-0.124-0.28510.85210.05750.638-13.42685.624911.8028
108.5615-2.43391.11538.0837-3.77038.723-0.59991.31870.1825-0.89680.4618-0.2709-0.0180.00090.15460.4064-0.1223-0.26240.7973-0.07590.6766-7.407610.91974.2749
111.14040.37850.560.52020.66571.37180.0132-0.0097-0.1195-0.2260.04930.05030.0687-0.1943-0.0190.1962-0.0351-0.2080.15070.02110.308516.889562.6257-47.4279
121.2318-0.0199-0.08781.26530.42261.23520.0933-0.07660.00620.09080.1032-0.3393-0.06720.26030.56110.1496-0.0258-0.24280.1138-0.15440.358527.794568.1444-37.055
130.366-0.03980.43831.39920.34141.29250.1348-0.0309-0.0831-0.1345-0.08390.04740.3085-0.1894-0.17250.1185-0.0144-0.19160.1457-0.01750.206312.299256.86-45.8972
146.491710.43832.3410.54333.3105-0.09340.80040.37410.1732-0.21810.1868-0.0641-0.3570.10260.18570.0149-0.0990.16930.02150.330512.388757.9946-48.2135
150.43820.1982-0.06140.50440.04910.02070.1894-0.0577-0.25810.1594-0.0787-0.190.274-0.15990.54150.1811-0.0405-0.31750.1919-0.04280.38518.402450.611-38.8157
162.10450.93940.432.18450.20811.5137-0.13710.429-0.3865-0.24050.2533-0.29650.03540.1764-0.06070.0832-0.2367-0.27210.1178-0.20580.2335-2.113133.8436-47.2748
171.5235-1.02090.81661.8424-0.46712.7265-0.03730.3534-0.17670.224-0.06770.1665-0.17150.14160.16280.18230.0219-0.14320.1388-0.05190.40530.842562.3717-67.7633
183.4138-0.51490.46194.2156-0.22981.54520.2033-0.05760.2558-0.2484-0.25830.187-0.1784-0.38930.02580.33320.1749-0.1150.2038-0.01670.3068-7.694267.7729-76.182
192.5104-0.91220.50072.75740.35634.05110.2593-0.12230.1209-0.0737-0.343-0.1937-0.1312-0.05560.13150.20530.0018-0.12960.1263-0.02380.26396.128254.1781-68.6585
200.8973-0.84610.04470.86680.1040.24050.0011-0.0399-0.1585-0.1679-0.09050.36460.0592-0.1603-0.0140.1852-0.0975-0.17050.14110.01790.46855.383347.3824-73.4625
213.22020.1948-0.33880.8004-0.05244.899-0.09080.1895-0.24750.06630.0003-0.15240.50420.1491-0.49680.44690.0757-0.25790.3703-0.03390.544724.514329.3108-69.4168
222.7551-0.5481.37193.33451.97133.8341-0.13170.0334-0.24880.24540.21840.18160.12670.4049-0.06510.1299-0.022-0.16080.19480.02660.263621.776938.4383-67.0741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 305 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 139 )
7X-RAY DIFFRACTION7chain 'B' and (resid 140 through 155 )
8X-RAY DIFFRACTION8chain 'B' and (resid 156 through 200 )
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 273 )
10X-RAY DIFFRACTION10chain 'B' and (resid 274 through 300 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 43 )
12X-RAY DIFFRACTION12chain 'C' and (resid 44 through 91 )
13X-RAY DIFFRACTION13chain 'C' and (resid 92 through 139 )
14X-RAY DIFFRACTION14chain 'C' and (resid 140 through 155 )
15X-RAY DIFFRACTION15chain 'C' and (resid 156 through 200 )
16X-RAY DIFFRACTION16chain 'C' and (resid 201 through 300 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 43 )
18X-RAY DIFFRACTION18chain 'D' and (resid 44 through 100 )
19X-RAY DIFFRACTION19chain 'D' and (resid 101 through 155 )
20X-RAY DIFFRACTION20chain 'D' and (resid 156 through 213 )
21X-RAY DIFFRACTION21chain 'D' and (resid 214 through 236 )
22X-RAY DIFFRACTION22chain 'D' and (resid 237 through 305 )

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  • 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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