1dne
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1dne |SIZE=350|CAPTION= <scene name='initialview01'>1dne</scene>, resolution 2.400Å | |PDB= 1dne |SIZE=350|CAPTION= <scene name='initialview01'>1dne</scene>, resolution 2.400Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NT:NETROPSIN'>NT</scene> | + | |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>, <scene name='pdbligand=NT:NETROPSIN'>NT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dne OCA], [http://www.ebi.ac.uk/pdbsum/1dne PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dne RCSB]</span> | ||
}} | }} | ||
| Line 27: | Line 30: | ||
[[Category: Rich, A.]] | [[Category: Rich, A.]] | ||
[[Category: Wang, A H.J.]] | [[Category: Wang, A H.J.]] | ||
| - | [[Category: NT]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''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 19:44:53 2008'' |
Revision as of 16:44, 30 March 2008
| |||||||
| , resolution 2.400Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2
Overview
The molecular structure of the complex between a minor groove binding drug (netropsin) and the DNA dodecamer d(CGCGATATCGCG) has been solved and refined by single-crystal X-ray diffraction analysis to a final R factor of 20.0% to 2.4-A resolution. The crystal is similar to that of the other related dodecamers with unit cell dimensions of a = 25.48 A, b = 41.26 A, and c = 66.88 A in the space group P2(1)2(1)2(1). In the complex, netropsin binds to the central ATAT tetranucleotide segment in the narrow minor groove of the dodecamer B-DNA double helix as expected. However, in the structural refinement the drug is found to fit the electron density in two orientations equally well, suggesting the disordered model. This agrees with the results from solution studies (chemical footprinting and NMR) of the interactions between minor groove binding drugs (e.g., netropsin and distamycin A) and DNA. The stabilizing forces between drug and DNA are provided by a combination of ionic, van der Waals, and hydrogen-bonding interactions. No bifurcated hydrogen bond is found between netropsin and DNA in this complex due to the unique dispositions of the hydrogen-bond acceptors (N3 of adenine and O2 of thymine) on the floor of the DNA minor groove. Two of the four AT base pairs in the ATAT stretch have low propeller twist angles, even though the DNA has a narrow minor groove. Alternating helical twist angles are observed in the ATAT stretch with lower twist in the ApT steps than in the TpA step.
About this Structure
1DNE is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment., Coll M, Aymami J, van der Marel GA, van Boom JH, Rich A, Wang AH, Biochemistry. 1989 Jan 10;28(1):310-20. PMID:2539859
Page seeded by OCA on Sun Mar 30 19:44:53 2008
