2neo
From Proteopedia
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|PDB= 2neo |SIZE=350|CAPTION= <scene name='initialview01'>2neo</scene> | |PDB= 2neo |SIZE=350|CAPTION= <scene name='initialview01'>2neo</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NCS:SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6-DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-INDACEN-2-ONE]]'>NCS</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=NCS:SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6-DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-INDACEN-2-ONE]]'>NCS</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2neo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2neo OCA], [http://www.ebi.ac.uk/pdbsum/2neo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2neo RCSB]</span> | ||
}} | }} | ||
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[[Category: Ji, J.]] | [[Category: Ji, J.]] | ||
[[Category: Stassinopoulos, A.]] | [[Category: Stassinopoulos, A.]] | ||
| - | [[Category: NCS]] | ||
[[Category: bulge binding ligand]] | [[Category: bulge binding ligand]] | ||
[[Category: bulge dna]] | [[Category: bulge dna]] | ||
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[[Category: enediyne antibiotics antitumor agent]] | [[Category: enediyne antibiotics antitumor agent]] | ||
| - | ''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 04:04:40 2008'' |
Revision as of 01:04, 31 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION NMR STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOG, 11 STRUCTURES
Overview
Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore in a base-catalyzed, radical-mediated reaction. The solution structure of the complex between an analog of the bulge-specific cleaving species and an oligodeoxynucleotide containing a two-base bulge was elucidated by nuclear magnetic resonance. An unusual binding mode involves major groove recognition by the drug carbohydrate unit and tight fitting of the wedge-shaped drug in the triangular prism pocket formed by the two looped-out bulge bases and the neighboring base pairs. The two drug rings mimic helical DNA bases, complementing the bent DNA structure. The putative abstracting drug radical is 2.2 +/- 0.1 angstroms from the pro-S H5' of the target bulge nucleotide. This structure clarifies the mechanism of bulge recognition and cleavage by a drug and provides insight into the design of bulge-specific nucleic acid binding molecules.
About this Structure
2NEO is a Protein complex structure of sequences from [1]. This structure supersedes the now removed PDB entry 1NEO. Full crystallographic information is available from OCA.
Reference
Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog., Stassinopoulos A, Ji J, Gao X, Goldberg IH, Science. 1996 Jun 28;272(5270):1943-6. PMID:8658168
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