1y8d
From Proteopedia
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|PDB= 1y8d |SIZE=350|CAPTION= <scene name='initialview01'>1y8d</scene> | |PDB= 1y8d |SIZE=350|CAPTION= <scene name='initialview01'>1y8d</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1eeg|1EEG]], [[1jjp|1JJP]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://www.ebi.ac.uk/pdbsum/1y8d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB]</span> | ||
}} | }} | ||
| Line 27: | Line 30: | ||
[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
[[Category: Phan, A T.]] | [[Category: Phan, A T.]] | ||
| - | [[Category: dimeric parallel-stranded quadruplex | + | [[Category: (a)gggg pentad]] |
| + | [[Category: 3+1 g-tetrad]] | ||
| + | [[Category: dimeric parallel-stranded quadruplex]] | ||
| + | [[Category: dna aptamer;hiv-1 integrase inhibitor design]] | ||
| + | [[Category: gag triad]] | ||
| + | [[Category: single nucleotide chain reversal loop]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:00:05 2008'' |
Revision as of 22:00, 30 March 2008
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| Ligands: | , , | ||||||
| Related: | 1EEG, 1JJP
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad
Overview
We report on the NMR-based solution structure of the 93del d(GGGGTGGGAGGAGGGT) aptamer, a potent nanomolar inhibitor of HIV-1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex architecture in K+ solution. Within each 16-nt monomer subunit, which contains one A.(G.G.G.G) pentad sandwiched between two G.G.G.G tetrads, all G-stretches are parallel, and all guanines are anti with the exception of G1, which is syn. Dimer formation is achieved through mutual pairing of G1 of one monomer, with G2, G6, and G13 of the other monomer, to complete G.G.G.G tetrad formation. There are three single-nucleotide double-chain-reversal loops within each monomer fold, such that the first (T5) and third (A12) loops bridge three G-tetrad layers, whereas the second (A9) loop bridges two G-tetrad layers and participates in A.(G.G.G.G) pentad formation. Results of NMR and of integrase inhibition assays on loop-modified sequences allowed us to propose a strategy toward the potential design of improved HIV-1 integrase inhibitors. Finally, we propose a model, based on molecular docking approaches, for positioning the 93del dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase.
About this Structure
1Y8D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase., Phan AT, Kuryavyi V, Ma JB, Faure A, Andreola ML, Patel DJ, Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):634-9. Epub 2005 Jan 6. PMID:15637158
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