1nyd
From Proteopedia
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|PDB= 1nyd |SIZE=350|CAPTION= <scene name='initialview01'>1nyd</scene> | |PDB= 1nyd |SIZE=350|CAPTION= <scene name='initialview01'>1nyd</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</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= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nyd OCA], [http://www.ebi.ac.uk/pdbsum/1nyd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nyd RCSB]</span> | ||
}} | }} | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Silva, M Webba da.]] | [[Category: Silva, M Webba da.]] | ||
| - | + | [[Category: double chain reversal,dna]] | |
| - | [[Category: double chain reversal]] | + | |
[[Category: molecular propeller topology]] | [[Category: molecular propeller topology]] | ||
[[Category: parallel quadruplex]] | [[Category: parallel quadruplex]] | ||
[[Category: quadruplex]] | [[Category: quadruplex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:37:12 2008'' |
Revision as of 19:37, 30 March 2008
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Solution structure of DNA quadruplex GCGGTGGAT
Overview
The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na(+) solution has been determined using molecular dynamics calculations constrained by distance and dihedral restraints derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has potential implications in genetic recombination. It suggests a pathway for oligomerization involving association of quadruplex entities through GpC steps.
About this Structure
1NYD is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT)., Webba da Silva M, Biochemistry. 2003 Dec 16;42(49):14356-65. PMID:14661946
Page seeded by OCA on Sun Mar 30 22:37:12 2008
