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Title: High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2      
description:
C-C motif chemokine 2
privacy:
not applicable
aggregation:
instance of dataset
ID:
PDB:4R8I
refinement:
curated
keywords:
Cytokine/RNA
Aptamer Spiegelmer L-oligonucleotide
Cytokine-RNA complex
creators:
Oberthur, D.
Achenbach, J.
Gabdulkhakov, A.
Buchner, K.
Maasch, C.
Falke, S.
Rehders, D.
Klussmann, S.
Betzel, C.
availability:
available
types:
structure
name:
Homo sapiens
ID:
ncbitax:9606
name:
Escherichia coli
ID:
ncbitax:562
authors:
Oberthur, D.
Achenbach, J.
Gabdulkhakov, A.
Buchner, K.
Maasch, C.
Falke, S.
Rehders, D.
Klussmann, S.
Betzel, C.
alternateID:
doi:10.1038/ncomms7923
year:
2015
ID: pmid:25901662
title:
Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2.
formula:
C4 H7 N O4
name:
ASPARTIC ACID
roles:
chemical component
formula:
C3 H7 N O2
name:
ALANINE
roles:
chemical component
formula:
C6 H13 N O2
name:
ISOLEUCINE
roles:
chemical component
formula:
C4 H8 N2 O3
name:
ASPARAGINE
roles:
chemical component
formula:
C5 H9 N O2
name:
PROLINE
roles:
chemical component
formula:
C5 H11 N O2
name:
VALINE
roles:
chemical component
formula:
C4 H9 N O3
name:
THREONINE
roles:
chemical component
formula:
C3 H7 N O2 S
name:
CYSTEINE
roles:
chemical component
formula:
C9 H11 N O3
name:
TYROSINE
roles:
chemical component
formula:
C9 H11 N O2
name:
PHENYLALANINE
roles:
chemical component
formula:
C6 H15 N4 O2 1
name:
ARGININE
roles:
chemical component
formula:
C6 H15 N2 O2 1
name:
LYSINE
roles:
chemical component
formula:
C3 H7 N O3
name:
SERINE
roles:
chemical component
formula:
C5 H10 N2 O3
name:
GLUTAMINE
roles:
chemical component
formula:
C6 H13 N O2
name:
LEUCINE
roles:
chemical component
formula:
C5 H9 N O4
name:
GLUTAMIC ACID
roles:
chemical component
formula:
C11 H12 N2 O2
name:
TRYPTOPHAN
roles:
chemical component
formula:
C5 H11 N O2 S
name:
METHIONINE
roles:
chemical component
formula:
C6 H10 N3 O2 1
name:
HISTIDINE
roles:
chemical component
formula:
C10 H14 N5 O8 P
name:
L-GUANOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C9 H14 N3 O8 P
name:
L-CYTIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C10 H14 N5 O7 P
name:
L-ADENOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C9 H13 N2 O9 P
name:
L-URIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C10 H15 N2 O8 P SE
name:
2'-METHYLSELENYL-2'-DEOXY-L-URIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
NA 1
name:
SODIUM ION
roles:
chemical component
formula:
SR 2
name:
STRONTIUM ION
roles:
chemical component
formula:
K 1
name:
POTASSIUM ION
roles:
chemical component
formula:
H2 O
name:
WATER
roles:
chemical component
name:
CCL2, MCP1, SCYA2
name:
X-RAY DIFFRACTION
ID:
pdb:4R8I
ID:
ndb:NA3256
ID:
rcsb:RCSB087032
accessURL: https://files.rcsb.org/download/4R8I.xml.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDBML/XML
accessType:
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authentication:
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authorization:
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accessURL: https://files.rcsb.org/download/4R8I.pdb.gz
storedIn:
Protein Data Bank
qualifier:
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license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
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accessType:
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authentication:
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authorization:
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accessURL: https://files.rcsb.org/download/4R8I.cif.gz
storedIn:
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qualifier:
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license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDBx/mmCIF
accessType:
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authentication:
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authorization:
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accessURL: http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=FASTA&compression=NO&structureId=4R8I
storedIn:
Protein Data Bank
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
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accessType:
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authentication:
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authorization:
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accessURL: https://files.rcsb.org/download/4R8I-sf.cif.gz
storedIn:
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qualifier:
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license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
CIF
accessType:
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authentication:
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authorization:
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accessURL: https://files.rcsb.org/download/4R8I.pdb1.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
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accessType:
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authentication:
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accessURL: http://www.rcsb.org/pdb/explore/jmol.do?structureId=4R8I&bionumber=1
storedIn:
Protein Data Bank
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
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accessType:
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authentication:
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authorization:
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abbreviation:
wwPDB
homePage: http://www.wwpdb.org
ID:
SCR:006555
name:
Worldwide Protein Data Bank
abbreviation:
PDB
homePage: http://www.rcsb.org/pdb/
ID:
SCR:012820
name:
Protein Data Bank