3LEX

2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex with HIV-1 GP41

> Summary

Summary for 3LEX

Related3LES 3LEV 3LEY 1TJI
Descriptor11f10 Antibody Heavy Chain, 11f10 Antibody Light Chain, Envelope glycoprotein gp41
Functional Keywordshiv-1, gp-41, monoclonal antibody, 2f5, scaffold, epitope, transplant, graft, re-elcitation, envelope protein, immune system, vaccine design
Biological sourceMus musculus (mouse)
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Total number of polymer chains6
Total molecular weight98334.47
Authors
Ofek, G.,Guenaga, F.J.,Schief, W.R.,Skinner, J.,Baker, D.,Wyatt, R.,Kwong, P.D. (deposition date: 2010-01-15, release date: 2010-09-29, modification date: 2010-11-24)
Primary citation
Ofek, G.,Guenaga, F.J.,Schief, W.R.,Skinner, J.,Baker, D.,Wyatt, R.,Kwong, P.D.
Elicitation of structure-specific antibodies by epitope scaffolds.
Proc.Natl.Acad.Sci.USA, 107:17880-17887, 2010
PubMed: 20876137
DOI: 10.1073/pnas.1004728107
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.97 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.19990.1%0.8%1.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

More Biological unit images

Molmil generated image of 3lex
no rotation
Molmil generated image of 3lex
rotated about x axis by 90°
Molmil generated image of 3lex
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (3lex.pdb1.gz [76.44 KB])
Coordinate files for Biological unit (3lex.pdb2.gz [76.59 KB])

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight98334.5
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight98334.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.97 Å)

Cell axes34.54370.96278.265
Cell angles90.0890.0290.29
SpacegroupP 1
Resolution limits25.90 - 1.97
the highest resolution shell value2.014 - 1.965
R-factor0.166
R-work0.16500
the highest resolution shell value0.185
R-free0.19800
the highest resolution shell value0.249
RMSD bond length0.009
RMSD bond angle0.892

Data Collection Statistics

Resolution limits25.90 - 1.96
the highest resolution shell value -
Number of reflections49925
Completeness94.6
I/sigma(I)5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP293

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
C0019031cellular_componentviral envelope
C0005198molecular_functionstructural molecule activity
P0019031cellular_componentviral envelope
P0005198molecular_functionstructural molecule activity
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Functional Information from PDB Data

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

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb3lex.ent.gz (154.5 KB)
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all (no-compress)pdb3lex.ent (628.7 KB)
header onlypdb3lex.ent.gz (7.11 KB)
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PDBx/mmCIF3lex.cif.gz (190.59 KB)
PDBMLall3lex.xml.gz (296.09 KB)
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no-atom3lex-noatom.xml.gz (38.95 KB)
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ext-atom3lex-extatom.xml.gz (175.14 KB)
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PDBMLplusall3lex-plus.xml.gz (296.97 KB)
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no-atom3lex-plus-noatom.xml.gz (39.83 KB)
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add only3lex-add.xml.gz (899 B)
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RDF3lex.rdf.gz (76.21 KB)
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Structure factorsr3lexsf.ent.gz (643.95 KB)
Biological unit (PDB format)3lex.pdb1.gz (76.44 KB) (P,H,L)
*author and software defined assembly, 3 molecule(s) (trimeric)
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3lex.pdb2.gz (76.59 KB) (C,A,B)
*author and software defined assembly, 3 molecule(s) (trimeric)
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Validation reportsPDF3lex​_validation.pdf.gz (282.55 KB)
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PDF-full3lex​_full​_validation.pdf.gz (293.9 KB)
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XML3lex​_validation.xml.gz (42.48 KB)
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PNG3lex​_multipercentile​_validation.png.gz (155.65 KB)
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SVG3lex​_multipercentile​_validation.svg.gz (947 B)
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Sequence (fasta)3lex​_seq.txt
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