1pqq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 4: Line 4:
|PDB= 1pqq |SIZE=350|CAPTION= <scene name='initialview01'>1pqq</scene>
|PDB= 1pqq |SIZE=350|CAPTION= <scene name='initialview01'>1pqq</scene>
|SITE=
|SITE=
-
|LIGAND= <scene name='pdbligand=CYE:45-(3-AMINOPROPYL)-5,11,22,28,34-PENTAMETHYL-3,9,15,20,26,32,38,43-OCTAOXO-2,5,8,14,19,22,25,28,31,34,37,42,45,48-TETRADECAAZA-11-AZONIAHEPTACYCLO[42.2.1.1~4,7~.1~10,13~.1~21,24~.1~27,30~.1~33,36~]DOPENTACONTA-1(46),4(52),6,10(51),12,21(50),23,27(49),29,33(48),35,44(47)-DODECAENE'>CYE</scene>
+
|LIGAND= <scene name='pdbligand=CYE:45-(3-AMINOPROPYL)-5,11,22,28,34-PENTAMETHYL-3,9,15,20,26,32,38,43-OCTAOXO-2,5,8,14,19,22,25,28,31,34,37,42,45,48-TETRADECAAZA-11-AZONIAHEPTACYCLO[42.2.1.1~4,7~.1~10,13~.1~21,24~.1~27,30~.1~33,36~]DOPENTACONTA-1(46),4(52),6,10(51),12,21(50),23,27(49),29,33(48),35,44(47)-DODECAENE'>CYE</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
|ACTIVITY=
|ACTIVITY=
|GENE=
|GENE=
 +
|DOMAIN=
 +
|RELATEDENTRY=
 +
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqq OCA], [http://www.ebi.ac.uk/pdbsum/1pqq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pqq RCSB]</span>
}}
}}
Line 28: Line 31:
[[Category: Wemmer, D E.]]
[[Category: Wemmer, D E.]]
[[Category: Zhang, Q.]]
[[Category: Zhang, Q.]]
-
[[Category: CYE]]
 
[[Category: dna]]
[[Category: dna]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:27:45 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:03:23 2008''

Revision as of 20:03, 30 March 2008

Image:1pqq.jpg


PDB ID 1pqq

Drag the structure with the mouse to rotate
Ligands: , , , ,
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



NMR Structure of a Cyclic Polyamide-DNA Complex


Overview

The solution structure of a cyclic polyamide ligand complexed to a DNA oligomer, derived from NMR restrained molecular mechanics, is presented. The polyamide, cyclo-gamma-ImPyPy-gamma-PyPyPy-, binds to target DNA with a nanomolar dissociation constant as characterized by quantitative footprinting previously reported. 2D (1)H NMR data were used to generate distance restraints defining the structure of this cyclic polyamide with the DNA duplex d(5'-GCCTGTTAGCG-3'):d(5'-CGCTAACAGGC-3'). Data interpretation used complete relaxation matrix analysis of the NOESY cross-peak intensities with the program MARDIGRAS. The NMR-based distance restraints (276 total) were applied in restrained molecular dynamics calculations using a solvent model, yielding structures with an rmsd for the ligand and binding site of approximately 1 A. The resulting structures indicate some distortion of the DNA in the binding site. The constraints from cyclization lead to altered stacking of the rings in the halves of the cyclic ligand relative to unlinked complexes. Despite this, the interactions with DNA are very similar to what has been found in unlinked complexes. Measurements of ligand amide and DNA imino proton exchange rates indicate very slow dissociation of the ligand and show that the DNA can undergo opening fluctuations while the ligand is bound although the presence of the ligand decreases their frequency relative to the free DNA.

About this Structure

1PQQ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

NMR structure of a cyclic polyamide-DNA complex., Zhang Q, Dwyer TJ, Tsui V, Case DA, Cho J, Dervan PB, Wemmer DE, J Am Chem Soc. 2004 Jun 30;126(25):7958-66. PMID:15212545

Page seeded by OCA on Sun Mar 30 23:03:23 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pqq"
Personal tools