198d
From Proteopedia
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|PDB= 198d |SIZE=350|CAPTION= <scene name='initialview01'>198d</scene>, resolution 1.970Å | |PDB= 198d |SIZE=350|CAPTION= <scene name='initialview01'>198d</scene>, resolution 1.970Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=DM5:IDARUBICIN'>DM5</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=DM5:IDARUBICIN'>DM5</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=198d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=198d OCA], [http://www.ebi.ac.uk/pdbsum/198d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=198d RCSB]</span> | ||
}} | }} | ||
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[[Category: Gallois, B.]] | [[Category: Gallois, B.]] | ||
[[Category: Hunter, W N.]] | [[Category: Hunter, W N.]] | ||
| - | [[Category: DM5]] | ||
| - | [[Category: SPM]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: right handed dna]] | [[Category: right handed dna]] | ||
| - | ''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 18:30:10 2008'' |
Revision as of 15:30, 30 March 2008
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| , resolution 1.970Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
A TRIGONAL FORM OF THE IDARUBICIN-D(CGATCG) COMPLEX: CRYSTAL AND MOLECULAR STRUCTURE AT 2.0 ANGSTROMS RESOLUTION
Overview
The X-ray crystal structure of the complex between the anthracycline idarubicin and d(CGATCG) has been solved by molecular replacement and refined to a resolution of 2.0 A. The final R-factor is 0.19 for 3768 reflections with Fo > or = 2 sigma (Fo). The complex crystallizes in the trigonal space group P31 with unit cell parameters a = b = 52.996(4), c = 33.065(2) A, alpha = beta = 90 degree, gamma = 120 degree. The asymmetric unit consists of two duplexes, each one being complexed with two idarubicin drugs intercalated at the CpG steps, one spermine and 160 water molecules. The molecular packing underlines major groove-major groove interactions between neighbouring helices, and an unusually low value of the occupied fraction of the unit cell due to a large solvent channel of approximately 30 A diameter. This is the first trigonal crystal form of a DNA-anthracycline complex. The structure is compared with the previously reported structure of the same complex crystallizing in a tetragonal form. The geometry of both the double helices and the intercalation site are conserved as are the intramolecular interactions despite the different crystal forms.
About this Structure
198D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A trigonal form of the idarubicin:d(CGATCG) complex; crystal and molecular structure at 2.0 A resolution., Dautant A, Langlois d'Estaintot B, Gallois B, Brown T, Hunter WN, Nucleic Acids Res. 1995 May 25;23(10):1710-6. PMID:7784175
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