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- PDB-7bgp: Crystal structure of MG-132 covalently bound to the main protease... -

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Basic information

Entry
Database: PDB / ID: 7bgp
TitleCrystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in absence of DTT.
ComponentsMain Protease
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Mpro / 3CLpro / EXSCALATE4COV / drug discovery / Elettra / MG-132
Function / homology
Function and homology information


Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / modulation by virus of host autophagy / RNA phosphodiester bond hydrolysis, exonucleolytic / mRNA methylation ...Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / modulation by virus of host autophagy / RNA phosphodiester bond hydrolysis, exonucleolytic / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / suppression by virus of host toll-like receptor signaling pathway / protein K48-linked deubiquitination / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / transcription, RNA-templated / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / viral genome replication / cysteine-type peptidase activity / suppression by virus of host TRAF activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / helicase activity / ubiquitinyl hydrolase 1 / Transferases; Transferring one-carbon groups; Methyltransferases / viral transcription / DNA helicase / methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / thiol-dependent deubiquitinase / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / suppression by virus of host type I interferon-mediated signaling pathway / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / Hydrolases; Acting on ester bonds / host cell cytoplasm / protein dimerization activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP1 superfamily, betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronaviral / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, middle domain / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus 2'-O-methyltransferase / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Betacoronavirus Nsp3c-M domain profile. / Coronaviridae zinc-binding (CV ZBD) domain profile. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein 6, betacoronavirus / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAR) / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Non-structural protein NSP3A domain-like superfamily / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Lipocalin signature. / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus endopeptidase C30 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP6 / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, N-terminal / Papain-like viral protease, palm and finger domains, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus-like / Peptidase C16, coronavirus / Peptidase C30, coronavirus / Peptidase C30, domain 3, coronavirus
Similarity search - Domain/homology
Chem-ALD / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsCostanzi, E. / Demitri, N. / Giabbai, B. / Storici, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101003551European Union
CitationJournal: To Be Published
Title: Crystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in absence of DTT.
Authors: Costanzi, E. / Demitri, N. / Giabbai, B. / Storici, P.
History
DepositionJan 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,28516
Polymers67,6512
Non-polymers1,63414
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-9 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.853, 99.779, 103.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Main Protease / pp1ab / ORF1ab polyprotein


Mass: 33825.547 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria)
References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 475 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ALD / N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide


Mass: 477.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12M Ethylene glycols (Diethylene glycol; Triethylene glycol; Tetraethylene glycol; Pentaethylene glycol) 0.1M Tris/BICINE pH 8.5, 20% v/v PEG 500 MME; 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→56.11 Å / Num. obs: 80614 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 21.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.5
Reflection shellResolution: 1.68→1.71 Å / Num. unique obs: 4098 / CC1/2: 0.604

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
PHENIX1.19_4085refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BB2

7bb2


Resolution: 1.68→45.94 Å / SU ML: 0.1966 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.3724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 3988 4.95 %
Rwork0.1704 76525 -
obs0.1719 80513 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.4 Å2
Refinement stepCycle: LAST / Resolution: 1.68→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 110 461 5258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994924
X-RAY DIFFRACTIONf_angle_d1.05516673
X-RAY DIFFRACTIONf_chiral_restr0.0583751
X-RAY DIFFRACTIONf_plane_restr0.0084865
X-RAY DIFFRACTIONf_dihedral_angle_d14.82431774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.32441570.30152718X-RAY DIFFRACTION99.93
1.7-1.720.33231400.28962694X-RAY DIFFRACTION99.93
1.72-1.740.30151620.28362702X-RAY DIFFRACTION99.97
1.74-1.770.33511310.27622695X-RAY DIFFRACTION99.89
1.77-1.790.28351320.27162716X-RAY DIFFRACTION100
1.79-1.820.28451280.24482709X-RAY DIFFRACTION99.79
1.82-1.850.28421450.23772748X-RAY DIFFRACTION100
1.85-1.880.25991500.22322656X-RAY DIFFRACTION99.93
1.88-1.910.23781550.20852696X-RAY DIFFRACTION100
1.91-1.950.23481420.19312725X-RAY DIFFRACTION99.9
1.95-1.980.24661610.19112684X-RAY DIFFRACTION100
1.98-2.020.18781380.19362722X-RAY DIFFRACTION99.93
2.02-2.070.24251480.18332714X-RAY DIFFRACTION99.97
2.07-2.120.20711560.17192737X-RAY DIFFRACTION99.97
2.12-2.170.20621480.16452686X-RAY DIFFRACTION99.96
2.17-2.230.19531390.15642695X-RAY DIFFRACTION99.96
2.23-2.290.17681380.15752757X-RAY DIFFRACTION99.93
2.29-2.370.18711610.15672723X-RAY DIFFRACTION99.97
2.37-2.450.184970.15762764X-RAY DIFFRACTION100
2.45-2.550.19311490.16162733X-RAY DIFFRACTION100
2.55-2.670.20221220.17182768X-RAY DIFFRACTION99.9
2.67-2.810.22661480.16972742X-RAY DIFFRACTION99.72
2.81-2.980.18441370.17442738X-RAY DIFFRACTION99.83
2.98-3.210.20741540.16972754X-RAY DIFFRACTION99.83
3.21-3.540.19051580.16022768X-RAY DIFFRACTION99.56
3.54-4.050.19061290.14222776X-RAY DIFFRACTION98.88
4.05-5.10.14051510.12372773X-RAY DIFFRACTION98.42
5.1-45.940.1791120.17222932X-RAY DIFFRACTION97.78
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)
13.130191333410.231959640357-0.730145150020.913553237135-0.1830792416452.74409516882-0.0127615327648-0.1131592289210.04273776539640.00957173902919-0.0161820016146-0.02725256495970.03917821844310.2423085827050.02568845937520.1683297086750.02289414403880.001565182783090.1290647760920.007386600138420.16276545910918.4084203999-6.82279650223-18.6266396724
22.73532374602-0.00545855646394-0.1985073536420.793543642605-1.164976241053.77765630037-0.089571681604-0.2203946346420.130567576610.0656394943365-0.142235095358-0.199199506251-0.09214565078030.5682720422670.2361671905420.1846302108670.014673456065-0.003239834291670.3570304192330.01828724125520.25467367563533.2378265497-5.49980122669-24.9659495232
33.4516726309-1.369656393283.093897594871.92997943732-2.038973340745.3470363012-0.124490844141-0.111034558723-0.1720884064950.03095497842460.0141155993185-0.0842045746610.1625165061960.1589923783590.008877656197060.190604155660.04888470226660.0249281343820.1255657751970.01693160035690.21217557444216.1776733231-15.8623238402-21.4652701796
43.044934707790.1118909726480.3879950361350.4839210102470.2455480179334.05509993542-0.0224032152952-0.07717116347250.07910327726040.008942304393-0.001782769356850.0176397183367-0.0001298468114140.06623703503710.03674110687340.164075457539-0.003311964461660.001707682020020.116855969194-0.002800296722690.18317954660211.5587999767-4.63209487976-23.3614475475
53.89647747290.626378556144-0.4785922705760.2063044730650.0179582053190.690628922479-0.02351631581190.2901695649040.208169054959-0.04707615452740.06054813563120.0295341343971-0.0790775118738-0.0413642278011-0.04861491389270.198962774465-0.00299164944878-0.007339044725330.1748612389450.0263461396230.1791569071247.36474214037-3.06732274666-33.6640730484
62.35789736794-0.3057475801450.05081537928391.8172432939-0.1062324459232.40059117282-0.01922820974120.03894179620710.0201932444040.05589108561010.01239370430710.123377059137-0.0455244621603-0.1542247888490.00807681897270.170269740587-0.00183759224351-0.003840649580160.2436323290290.001792231086340.214630751497-12.4555961324-6.84048308314-33.8534554538
71.973840272530.412242831349-0.11576116193.41764875342-1.53180750843.479276472840.1230929289610.0846355765898-0.0268325862113-0.105596451026-0.05868402710780.1464298241430.293125741899-0.102331923154-0.04599629344550.176722061559-0.01787193669660.0174017216550.136888509049-0.0080453896890.1677075953634.03082643425-6.87075915841-8.29784450213
82.45026540467-1.005796033511.628764848931.7385872515-0.4400089122193.94803394610.0358438123937-0.416587581987-0.2557329688090.05425968824060.1136072407870.2029708694190.331427074891-0.684300371628-0.03324564603810.184456440475-0.07468184976520.03443957861790.2649772751750.04996462721260.184723851932-4.70398238994-9.88467198061.84286409887
90.808920969121-0.238782831069-0.1433383929521.6482989732-1.192268070542.308825531130.0340171320080.05195593918840.0604751361990.1014395832950.1464154775870.031303276551-0.355116133224-0.509108101402-0.1392374769620.2016159367120.05524851571660.01309944677550.225388033611-0.02846009715230.179010173363-7.8082404822412.2704053991-12.9136052169
102.8914358388-0.451233124373-1.290096600542.58083282124-0.4778096238413.520488436780.0851312567058-0.05678544204850.2456622511450.142980806090.07201309205890.0442010162164-0.866643612704-0.0608984074846-0.1170374684480.3809919046480.007193094085130.04442966000280.194979404214-0.02976533013530.219141451688-3.4944769262518.0535446158-15.227714938
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )AA1 - 431 - 43
22chain 'A' and (resid 44 through 91 )AA44 - 9144 - 91
33chain 'A' and (resid 92 through 110 )AA92 - 11092 - 110
44chain 'A' and (resid 111 through 166 )AA111 - 166111 - 166
55chain 'A' and (resid 167 through 213 )AA167 - 213167 - 213
66chain 'A' and (resid 214 through 301 )AA214 - 301214 - 301
77chain 'B' and (resid 1 through 22 )BJ1 - 221 - 22
88chain 'B' and (resid 23 through 180 )BJ23 - 18023 - 180
99chain 'B' and (resid 181 through 226 )BJ181 - 226181 - 226
1010chain 'B' and (resid 227 through 305 )BJ227 - 305227 - 305

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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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