3Q6R

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with disordered HBGA type Lex

> Summary

Summary for 3Q6R

Related3ONY 3ONU 3PA1 3PA2 3R6J 3R6K 3Q38 3Q39 3Q3A 3Q6Q
DescriptorCapsid protein
Functional Keywordsnorovirus, p-domain, capsid, receptor, histo blood group antigen (hbga), viral protein
Biological sourceNorwalk virus
Total number of polymer chains2
Total molecular weight71066.18
Authors
Hansman, G.S.,Biertumpfel, C.,McLellan, J.S.,Chen, L.,Georgiev, I.,Katayama, K.,Kwong, P.D. (deposition date: 2011-01-03, release date: 2011-05-11, modification date: 2011-11-02)
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 (1.4 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.17650.2%0.4%4.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3q6r
no rotation
Molmil generated image of 3q6r
rotated about x axis by 90°
Molmil generated image of 3q6r
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BCapsid proteinpolymer31934805.32
UniProt (Q5F4T5)
Pfam (PF00915)
Pfam (PF08435)
Norwalk virus
1,2-ETHANEDIOLnon-polymer62.119
IMIDAZOLEnon-polymer69.14
waterwater18.0967

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight69610.5
Non-Polymers*Number of molecules23
Total molecular weight1455.6
All*Total molecular weight71066.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.4 Å)

Cell axes65.28079.02469.703
Cell angles90.0099.8790.00
SpacegroupP 1 21 1
Resolution limits26.67 - 1.40
the highest resolution shell value1.416 - 1.400
R-factor0.1654
R-work0.16480
the highest resolution shell value0.265
R-free0.17790
the highest resolution shell value0.278
RMSD bond length0.006
RMSD bond angle1.062

Data Collection Statistics

Resolution limits26.67 - 1.40
the highest resolution shell value -
Number of reflections136423
Completeness99.6
Redundancy3.73
the highest resolution shell value3.67
I/sigma(I)-3

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 B 1
ChainResidue
BHOH42
BHOH137
BLEU279
BTHR281
BARG287

AC27BINDING SITE FOR RESIDUE EDO A 2
ChainResidue
AHOH35
AHOH92
APRO245
AILE246
AHOH600
BHOH137
BASN311

AC37BINDING SITE FOR RESIDUE EDO B 3
ChainResidue
BHOH19
BHOH37
BHOH166
BASN309
BLEU310
BASN311
BLEU325

AC45BINDING SITE FOR RESIDUE EDO B 4
ChainResidue
BHOH101
BHOH115
BGLU464
BHIS468
BHOH597

AC56BINDING SITE FOR RESIDUE EDO A 5
ChainResidue
AHOH134
APRO230
AGLU464
AHIS468
AHOH618
BHOH101

AC66BINDING SITE FOR RESIDUE EDO B 6
ChainResidue
AHOH104
APHE445
APRO447
BARG341
BHOH539
BHOH583

AC78BINDING SITE FOR RESIDUE EDO A 7
ChainResidue
AEDO8
AHOH60
AHOH147
APHE408
AGLN410
APRO455
AALA456
AHOH749

AC89BINDING SITE FOR RESIDUE EDO A 8
ChainResidue
AEDO7
ATYR250
AASN252
AGLU255
AGLN410
ATRP411
AARG443
AHOH855
AHOH966

AC96BINDING SITE FOR RESIDUE EDO A 9
ChainResidue
AHOH65
AHOH113
ALEU279
ATHR281
AARG287
ALEU310

BC17BINDING SITE FOR RESIDUE EDO A 10
ChainResidue
AHOH31
AHOH34
AHOH158
AASN309
ALEU310
AASN311
ALEU325

BC23BINDING SITE FOR RESIDUE EDO B 11
ChainResidue
BSER379
BTHR380
BHOH618

BC37BINDING SITE FOR RESIDUE EDO A 12
ChainResidue
APRO317
ATHR318
AGLU319
AASP320
ALYS372
AMET424
AASN425

BC46BINDING SITE FOR RESIDUE EDO A 13
ChainResidue
AGLN277
ALEU278
AHOH603
AHOH931
BHOH119
BGLU236

BC510BINDING SITE FOR RESIDUE EDO A 14
ChainResidue
AHOH39
AHOH48
AHOH130
AHOH150
APRO243
APRO280
ATHR281
BPRO243
BPRO280
BTHR281

BC69BINDING SITE FOR RESIDUE EDO B 15
ChainResidue
AIMD23
AGLU359
ALYS449
BHOH46
BHIS358
BGLU359
BTRP381
BHOH718
BHOH814

BC79BINDING SITE FOR RESIDUE EDO A 16
ChainResidue
AHOH40
AHIS358
AGLU359
ATRP381
AHOH873
AHOH961
BIMD22
BGLU359
BLYS449

BC85BINDING SITE FOR RESIDUE EDO A 17
ChainResidue
AHOH70
AGLU236
AHOH667
BLEU278
BLEU325

BC96BINDING SITE FOR RESIDUE EDO A 18
ChainResidue
AARG299
AGLY300
ASER379
ATHR380
AHOH841
AHOH894

CC17BINDING SITE FOR RESIDUE EDO A 19
ChainResidue
AGLY451
ATYR452
AHOH681
AHOH953
AHOH956
BALA354
BASN355

CC25BINDING SITE FOR RESIDUE IMD B 20
ChainResidue
BLEU272
BGLN273
BGLY274
BTHR276
BHOH770

CC35BINDING SITE FOR RESIDUE IMD A 21
ChainResidue
ALEU272
AGLN273
AGLY274
ATHR276
AHOH631

CC45BINDING SITE FOR RESIDUE IMD B 22
ChainResidue
AEDO16
AHIS358
BGLU359
BTRP381
BLYS449

CC56BINDING SITE FOR RESIDUE IMD A 23
ChainResidue
AGLU359
ATRP381
ALYS449
BEDO15
BHIS358
BHOH814

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

site_idNumber of ResiduesDetails
EDO_3q6r_A_581,2-ETHANEDIOL binding site
ChainResidueligand
APRO230EDO: 1,2-ETHANEDIOL
ALEU232EDO: 1,2-ETHANEDIOL
AGLU464EDO: 1,2-ETHANEDIOL
AGLN467-HIS468EDO: 1,2-ETHANEDIOL
BGLN467-HIS468EDO: 1,2-ETHANEDIOL
BGLN471EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_291,2-ETHANEDIOL binding site
ChainResidueligand
ALEU234-GLY235EDO: 1,2-ETHANEDIOL
APRO245-ASP247EDO: 1,2-ETHANEDIOL
BLEU279EDO: 1,2-ETHANEDIOL
BARG287EDO: 1,2-ETHANEDIOL
BLEU310-ASN311EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_1771,2-ETHANEDIOL binding site
ChainResidueligand
AGLU236EDO: 1,2-ETHANEDIOL
BLEU272EDO: 1,2-ETHANEDIOL
BTHR276-LEU278EDO: 1,2-ETHANEDIOL
BLEU325EDO: 1,2-ETHANEDIOL
BTYR470EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_1461,2-ETHANEDIOL binding site
ChainResidueligand
APRO243EDO: 1,2-ETHANEDIOL
APRO280-THR281EDO: 1,2-ETHANEDIOL
BPRO243EDO: 1,2-ETHANEDIOL
BPRO280-THR281EDO: 1,2-ETHANEDIOL

EDO_3q6r_B_1101,2-ETHANEDIOL binding site
ChainResidueligand
APRO245EDO: 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_3q6r_A_871,2-ETHANEDIOL binding site
ChainResidueligand
ATYR250EDO: 1,2-ETHANEDIOL
AASN252EDO: 1,2-ETHANEDIOL
AGLU255EDO: 1,2-ETHANEDIOL
AGLN410-TRP411EDO: 1,2-ETHANEDIOL
AARG443EDO: 1,2-ETHANEDIOL
AASP458EDO: 1,2-ETHANEDIOL

IMD_3q6r_A_217IMIDAZOLE binding site
ChainResidueligand
ALEU272-THR276IMD: IMIDAZOLE
AVAL321IMD: IMIDAZOLE
ALEU325IMD: IMIDAZOLE

EDO_3q6r_A_1381,2-ETHANEDIOL binding site
ChainResidueligand
ALEU272EDO: 1,2-ETHANEDIOL
ATHR276-LEU279EDO: 1,2-ETHANEDIOL
ALEU325EDO: 1,2-ETHANEDIOL
ATYR470EDO: 1,2-ETHANEDIOL
BGLU236EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_1051,2-ETHANEDIOL binding site
ChainResidueligand
AGLN277EDO: 1,2-ETHANEDIOL
AASN309-ASN311EDO: 1,2-ETHANEDIOL
ALEU325EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_9101,2-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
BPRO245EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_1861,2-ETHANEDIOL binding site
ChainResidueligand
AARG299-GLY300EDO: 1,2-ETHANEDIOL
AVAL361EDO: 1,2-ETHANEDIOL
ASER379-TRP381EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_1281,2-ETHANEDIOL binding site
ChainResidueligand
APRO317-VAL321EDO: 1,2-ETHANEDIOL
ALYS372EDO: 1,2-ETHANEDIOL
AMET424-ASN425EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_1671,2-ETHANEDIOL binding site
ChainResidueligand
AALA357-GLU359EDO: 1,2-ETHANEDIOL
ATRP381-GLU382EDO: 1,2-ETHANEDIOL
BGLU359EDO: 1,2-ETHANEDIOL
BLYS449EDO: 1,2-ETHANEDIOL

IMD_3q6r_B_226IMIDAZOLE binding site
ChainResidueligand
AALA357-HIS358IMD: IMIDAZOLE
AGLU382IMD: IMIDAZOLE
BGLU359IMD: IMIDAZOLE
BTRP381IMD: IMIDAZOLE
BLYS449IMD: IMIDAZOLE

EDO_3q6r_B_1571,2-ETHANEDIOL binding site
ChainResidueligand
AGLU359EDO: 1,2-ETHANEDIOL
ALYS449EDO: 1,2-ETHANEDIOL
BALA357-GLU359EDO: 1,2-ETHANEDIOL
BTRP381-GLU382EDO: 1,2-ETHANEDIOL

IMD_3q6r_A_236IMIDAZOLE binding site
ChainResidueligand
AGLU359IMD: IMIDAZOLE
ATRP381IMD: IMIDAZOLE
ALYS449IMD: IMIDAZOLE
BALA357-HIS358IMD: IMIDAZOLE
BGLU382IMD: IMIDAZOLE

EDO_3q6r_A_781,2-ETHANEDIOL binding site
ChainResidueligand
APHE408EDO: 1,2-ETHANEDIOL
AGLN410EDO: 1,2-ETHANEDIOL
AARG443EDO: 1,2-ETHANEDIOL
AASN454-ASP458EDO: 1,2-ETHANEDIOL

EDO_3q6r_B_671,2-ETHANEDIOL binding site
ChainResidueligand
APHE445-PRO447EDO: 1,2-ETHANEDIOL
AASN454EDO: 1,2-ETHANEDIOL
BARG287EDO: 1,2-ETHANEDIOL
BARG341EDO: 1,2-ETHANEDIOL
BLYS393EDO: 1,2-ETHANEDIOL

EDO_3q6r_A_1961,2-ETHANEDIOL binding site
ChainResidueligand
AGLY450-TYR452EDO: 1,2-ETHANEDIOL
BALA354-ARG356EDO: 1,2-ETHANEDIOL

EDO_3q6r_B_471,2-ETHANEDIOL binding site
ChainResidueligand
AGLN467EDO: 1,2-ETHANEDIOL
AGLN471EDO: 1,2-ETHANEDIOL
BPRO230EDO: 1,2-ETHANEDIOL
BLEU232EDO: 1,2-ETHANEDIOL
BGLU464EDO: 1,2-ETHANEDIOL
BGLN467-HIS468EDO: 1,2-ETHANEDIOL

IMD_3q6r_B_207IMIDAZOLE binding site
ChainResidueligand
BLEU272-THR276IMD: IMIDAZOLE
BVAL321IMD: IMIDAZOLE
BLEU325IMD: IMIDAZOLE

EDO_3q6r_B_351,2-ETHANEDIOL binding site
ChainResidueligand
BGLN277EDO: 1,2-ETHANEDIOL
BASN309-ASN311EDO: 1,2-ETHANEDIOL
BLEU325EDO: 1,2-ETHANEDIOL

EDO_3q6r_B_1151,2-ETHANEDIOL binding site
ChainResidueligand
BGLY300EDO: 1,2-ETHANEDIOL
BVAL361EDO: 1,2-ETHANEDIOL
BSER379-TRP381EDO: 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
SWS_FT_FI12Fucose.
ChainResidueDetails
ATRP162
AASP166

SWS_FT_FI21N-acetyl-D-glucosamine; via carbonyl oxygen.
ChainResidueDetails
ALYS230

SWS_FT_FI31Galactose.
ChainResidueDetails
AARG80

SWS_FT_FI41N-acetyl-D-glucosamine.
ChainResidueDetails
AGLU163

SWS_FT_FI52Fucose.
ChainResidueDetails
BTRP162
BASP166

SWS_FT_FI61N-acetyl-D-glucosamine; via carbonyl oxygen.
ChainResidueDetails
BLYS230

SWS_FT_FI71Galactose.
ChainResidueDetails
BNA*

SWS_FT_FI81N-acetyl-D-glucosamine.
ChainResidueDetails
BGLU163

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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