3LES

2F5 Epitope scaffold ES2

> Summary

Summary for 3LES

Related3LEV 3LEX 3LEY 1TJI
DescriptorRNA polymerase sigma factor
Functional Keywordshiv-1, gp41, monoclonal antibody, 2f5, epitope, transplant, scaffold, graft, sigma factor, re-elicitation, immune system, vaccine design
Biological sourceThermus aquaticus
Total number of polymer chains2
Total molecular weight40803.24
Authors
Ofek, G.,Guenaga, F.J.,Schief, W.R.,Skinner, J.,Wyatt, R.,Baker, D.,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 (2.77 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.246151.4%3.8%17.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

More Biological unit images

Molmil generated image of 3les
no rotation
Molmil generated image of 3les
rotated about x axis by 90°
Molmil generated image of 3les
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 (3les.pdb1.gz [62.41 KB])
Coordinate files for Biological unit (3les.pdb2.gz [61.39 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BRNA polymerase sigma factorpolymer17920209.52
UniProt (Q9EZJ8)
Pfam (PF00140)
Pfam (PF04542)
Thermus aquaticus
SULFATE IONnon-polymer96.14
waterwater18.028

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight40419.0
Non-Polymers*Number of molecules4
Total molecular weight384.2
All*Total molecular weight40803.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.77 Å)

Cell axes37.25749.98757.567
Cell angles78.0389.8387.57
SpacegroupP 1
Resolution limits48.85 - 2.77
the highest resolution shell value -
R-factor0.23
R-work0.22700
R-free0.26000
RMSD bond length0.004
RMSD bond angle0.751

Data Collection Statistics

Resolution limits50.00 - 2.77
the highest resolution shell value -
Number of reflections9968
Completeness95.9
Redundancy1.8
the highest resolution shell value1.7
I/sigma(I)4

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

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
A0005737cellular_componentcytoplasm
A0003677molecular_functionDNA binding
A0016987molecular_functionsigma factor activity
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0001123biological_processtranscription initiation from bacterial-type RNA polymerase promoter
B0005737cellular_componentcytoplasm
B0003677molecular_functionDNA binding
B0016987molecular_functionsigma factor activity
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0001123biological_processtranscription initiation from bacterial-type RNA polymerase promoter
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC11BINDING SITE FOR RESIDUE SO4 A 1
ChainResidue
AARG237

AC27BINDING SITE FOR RESIDUE SO4 A 2
ChainResidue
AHOH9
ATHR153
AALA154
AALA155
AHIS201
AGLU204
BSER223

AC36BINDING SITE FOR RESIDUE SO4 A 3
ChainResidue
AHOH17
ALYS158
APRO160
AGLY161
ALEU162
AGLN229

AC47BINDING SITE FOR RESIDUE SO4 B 4
ChainResidue
ASER223
BHOH2
BTHR153
BALA154
BALA155
BHIS201
BGLU204

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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

site_idNumber of ResiduesDetails
PS008672Carbamoyl-phosphate synthase subdomain signature 2. [LIVMF]-[LIMN]-E-[LIVMCA]-N-[PATLIVM]-[KR]-[LIVMSTAC]
ChainResidueDetails
ANA*
BNA*

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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)
PDBallpdb3les.ent.gz (126.93 KB)
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all (no-compress)pdb3les.ent (494.46 KB)
header onlypdb3les.ent.gz (6.76 KB)
Display
PDBx/mmCIF3les.cif.gz (154.75 KB)
PDBMLall3les.xml.gz (233.27 KB)
Display
no-atom3les-noatom.xml.gz (19.71 KB)
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ext-atom3les-extatom.xml.gz (68.65 KB)
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PDBMLplusall3les-plus.xml.gz (234.67 KB)
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no-atom3les-plus-noatom.xml.gz (21.12 KB)
Display
add only3les-add.xml.gz (1.41 KB)
Display
RDF3les.rdf.gz (36.28 KB)
Display
Structure factorsr3lessf.ent.gz (71.39 KB)
Biological unit (PDB format)3les.pdb1.gz (62.41 KB) (A)
*author and software defined assembly, 1 molecule(s) (monomeric)
Display
3les.pdb2.gz (61.39 KB) (B)
*author and software defined assembly, 1 molecule(s) (monomeric)
Display
Validation reportsPDF3les​_validation.pdf.gz (275.37 KB)
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PDF-full3les​_full​_validation.pdf.gz (286.61 KB)
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XML3les​_validation.xml.gz (17.02 KB)
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PNG3les​_multipercentile​_validation.png.gz (152.14 KB)
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SVG3les​_multipercentile​_validation.svg.gz (952 B)
Display
Sequence (fasta)3les​_seq.txt
Display

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