6bna
From Proteopedia
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|PDB= 6bna |SIZE=350|CAPTION= <scene name='initialview01'>6bna</scene>, resolution 2.210Å | |PDB= 6bna |SIZE=350|CAPTION= <scene name='initialview01'>6bna</scene>, resolution 2.210Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NT:NETROPSIN'>NT</scene> | + | |LIGAND= <scene name='pdbligand=CBR:5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>CBR</scene>, <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=6bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bna OCA], [http://www.ebi.ac.uk/pdbsum/6bna PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=6bna RCSB]</span> | ||
}} | }} | ||
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[[Category: Pjura, P.]] | [[Category: Pjura, P.]] | ||
[[Category: Yoon, C.]] | [[Category: Yoon, C.]] | ||
| - | [[Category: NT]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
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[[Category: modified]] | [[Category: modified]] | ||
| - | ''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 05:42:40 2008'' |
Revision as of 02:42, 31 March 2008
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| , resolution 2.210Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G
Overview
The antitumor antibiotic netropsin has been co-crystallized with a double-helical B-DNA dodecanucleotide of sequence: C-G-C-G-A-A-T-T-BrC-G-C-G, and the structure of the complex has been solved by X-ray diffraction at a resolution of 2.2 A. The structure has been refined independently by Jack-Levitt and Hendrickson-Konnert least-squares methods, leading to a final residual error of 0.257 by the Jack-Levitt approach (0.211 for two-sigma data) or 0.248 by the Hendrickson-Konnert approach, with no significant difference between refined structures. The netropsin molecule displaces the spine of hydration and fits snugly within the minor groove in the A-A-T-T center. It widens the groove slightly and bends the helix axis back by 8 degrees, but neither unwinds nor elongates the double helix. The drug molecule is held in place by amide NH hydrogen bonds that bridge adenine N-3 and thymine O-2 atoms, exactly as with the spine of hydration. The requirement of A X T base-pairs in the binding site arises because the N-2 amino group of guanine would demand impermissibly close contacts with netropsin. It is proposed that substitution of imidazole for pyrrole in netropsin should create a family of "lexitropsins" capable of reading G X C-containing base sequences.
About this Structure
6BNA is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G., Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE, J Mol Biol. 1985 Jun 25;183(4):553-63. PMID:2991536
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