3ONU

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026

> Summary

Summary for 3ONU

Related3ONY
DescriptorCapsid protein
Functional Keywordsviral capsid domain, viral protein
Biological sourceNorwalk virus
Total number of polymer chains2
Total molecular weight69932.93
Authors
Hansman, G.S.,Biertumpfel, C.,Chen, L.,Georgiev, I.,McLellan, J.S.,Katayama, K.,Kwong, P.D. (deposition date: 2010-08-30, release date: 2011-05-11, modification date: 2011-06-22)
Primary citation
Hansman, G.S.,Biertumpfel, C.,Georgiev, I.,McLellan, J.S.,Chen, L.,Zhou, T.,Katayama, K.,Kwong, P.D.
Crystal Structures of GII.10 and GII.12 Norovirus Protruding Domains in Complex with Histo-Blood Group Antigens Reveal Details for a Potential Site of Vulnerability.
J.Virol., 85:6687-6701, 2011
PubMed: 21525337
DOI: 10.1128/JVI.00246-11
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.395 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.16430.2%0.4%5.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3onu
no rotation
Molmil generated image of 3onu
rotated about x axis by 90°
Molmil generated image of 3onu
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BCapsid proteinpolymer31834718.22
UniProt (Q5F4T5)
Pfam (PF00915)
Pfam (PF08435)
Norwalk virus
1,2-ETHANEDIOLnon-polymer62.18
waterwater18.0909

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight69436.4
Non-Polymers*Number of molecules8
Total molecular weight496.5
All*Total molecular weight69932.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.395 Å)

Cell axes65.21779.11169.292
Cell angles90.0099.6590.00
SpacegroupP 1 21 1
Resolution limits22.70 - 1.40
the highest resolution shell value1.411 - 1.396
R-factor0.1514
R-work0.15050
the highest resolution shell value0.224
R-free0.16720
the highest resolution shell value0.235
RMSD bond length0.011
RMSD bond angle1.331

Data Collection Statistics

Resolution limits50.00 - 1.40
the highest resolution shell value -
Number of reflections130975
the highest resolution shell value0.449
Completeness95.2
the highest resolution shell value2.7
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15BINDING SITE FOR RESIDUE EDO A 2
ChainResidue
AHOH90
AHOH140
ATHR281
AGLY282
ALEU310

AC27BINDING SITE FOR RESIDUE EDO A 3
ChainResidue
AHOH29
AHOH37
AHOH181
AASN309
ALEU310
AASN311
ALEU325

AC35BINDING SITE FOR RESIDUE EDO A 4
ChainResidue
AHOH165
AGLU464
AHIS468
AHOH606
BHOH118

AC48BINDING SITE FOR RESIDUE EDO A 7
ChainResidue
AARG299
AGLY300
ASER379
ATHR380
ATRP381
AHOH703
AHOH819
AHOH851

AC56BINDING SITE FOR RESIDUE EDO B 1
ChainResidue
BHOH75
BHOH169
BLEU279
BTHR281
BGLY282
BARG287

AC67BINDING SITE FOR RESIDUE EDO B 5
ChainResidue
BHOH20
BHOH42
BASN309
BLEU310
BASN311
BLEU325
BHOH544

AC76BINDING SITE FOR RESIDUE EDO B 6
ChainResidue
AGLN471
BHOH114
BHOH118
BGLU464
BHIS468
BHOH788

AC84BINDING SITE FOR RESIDUE EDO B 8
ChainResidue
AHOH115
APRO447
BARG341
BHOH568

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_3onu_A_491,2-ETHANEDIOL binding site
ChainResidueligand
APRO230EDO: 1,2-ETHANEDIOL
ALEU232EDO: 1,2-ETHANEDIOL
AGLU464-TRP465EDO: 1,2-ETHANEDIOL
AGLN467-HIS468EDO: 1,2-ETHANEDIOL
BGLN467-HIS468EDO: 1,2-ETHANEDIOL
BGLN471EDO: 1,2-ETHANEDIOL

EDO_3onu_B_5101,2-ETHANEDIOL binding site
ChainResidueligand
AGLY235EDO: 1,2-ETHANEDIOL
BGLN277EDO: 1,2-ETHANEDIOL
BLEU279EDO: 1,2-ETHANEDIOL
BASN309-THR313EDO: 1,2-ETHANEDIOL
BLEU325-GLY326EDO: 1,2-ETHANEDIOL

EDO_3onu_B_1121,2-ETHANEDIOL binding site
ChainResidueligand
ATHR238EDO: 1,2-ETHANEDIOL
ALEU244-PRO245EDO: 1,2-ETHANEDIOL
BLEU279EDO: 1,2-ETHANEDIOL
BTHR281-GLY282EDO: 1,2-ETHANEDIOL
BALA285-ARG287EDO: 1,2-ETHANEDIOL
BLEU310EDO: 1,2-ETHANEDIOL
BLYS393-PHE394EDO: 1,2-ETHANEDIOL

EDO_3onu_B_8121,2-ETHANEDIOL binding site
ChainResidueligand
ALEU244EDO: 1,2-ETHANEDIOL
APHE445-LEU448EDO: 1,2-ETHANEDIOL
AASN454-PRO455EDO: 1,2-ETHANEDIOL
BARG287EDO: 1,2-ETHANEDIOL
BSER339EDO: 1,2-ETHANEDIOL
BARG341EDO: 1,2-ETHANEDIOL
BASN355EDO: 1,2-ETHANEDIOL
BLYS393EDO: 1,2-ETHANEDIOL

EDO_3onu_A_3111,2-ETHANEDIOL binding site
ChainResidueligand
AGLN277-LEU279EDO: 1,2-ETHANEDIOL
AASN309-THR313EDO: 1,2-ETHANEDIOL
ALEU325-GLY326EDO: 1,2-ETHANEDIOL
BGLY235EDO: 1,2-ETHANEDIOL

EDO_3onu_A_2121,2-ETHANEDIOL binding site
ChainResidueligand
ALEU279EDO: 1,2-ETHANEDIOL
ATHR281-GLY282EDO: 1,2-ETHANEDIOL
AALA285-ARG287EDO: 1,2-ETHANEDIOL
ALEU310EDO: 1,2-ETHANEDIOL
ALYS393-PHE394EDO: 1,2-ETHANEDIOL
BTHR238EDO: 1,2-ETHANEDIOL
BLEU244-PRO245EDO: 1,2-ETHANEDIOL

EDO_3onu_A_781,2-ETHANEDIOL binding site
ChainResidueligand
AARG299-THR301EDO: 1,2-ETHANEDIOL
AALA360-VAL361EDO: 1,2-ETHANEDIOL
ASER379-TRP381EDO: 1,2-ETHANEDIOL

EDO_3onu_B_691,2-ETHANEDIOL binding site
ChainResidueligand
AGLN467-HIS468EDO: 1,2-ETHANEDIOL
AGLN471EDO: 1,2-ETHANEDIOL
BPRO230EDO: 1,2-ETHANEDIOL
BLEU232EDO: 1,2-ETHANEDIOL
BGLU464-TRP465EDO: 1,2-ETHANEDIOL
BGLN467-HIS468EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb3onu.ent.gz (314.11 KB)
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all (no-compress)pdb3onu.ent (1.24 MB)
header onlypdb3onu.ent.gz (8.45 KB)
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PDBx/mmCIF3onu.cif.gz (376.81 KB)
PDBMLall3onu.xml.gz (565.87 KB)
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no-atom3onu-noatom.xml.gz (39.04 KB)
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ext-atom3onu-extatom.xml.gz (238.65 KB)
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PDBMLplusall3onu-plus.xml.gz (567.98 KB)
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no-atom3onu-plus-noatom.xml.gz (41.14 KB)
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add only3onu-add.xml.gz (2.11 KB)
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RDF3onu.rdf.gz (71.91 KB)
Display
Structure factorsr3onusf.ent.gz (1.51 MB)
Biological unit (PDB format)3onu.pdb1.gz (307.61 KB) (A,B)
*author defined assembly, 2 molecule(s) (dimeric)
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3onu.pdb2.gz (156.28 KB) (A)
*software defined assembly, 1 molecule(s) (monomeric)
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3onu.pdb3.gz (154.92 KB) (B)
*software defined assembly, 1 molecule(s) (monomeric)
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Validation reportsPDF3onu​_validation.pdf.gz (280.47 KB)
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PDF-full3onu​_full​_validation.pdf.gz (284.58 KB)
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XML3onu​_validation.xml.gz (35.7 KB)
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PNG3onu​_multipercentile​_validation.png.gz (156.72 KB)
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SVG3onu​_multipercentile​_validation.svg.gz (946 B)
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Sequence (fasta)3onu​_seq.txt
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