1dvl
From Proteopedia
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| - | [[Image:1dvl.gif|left|200px]] | + | [[Image:1dvl.gif|left|200px]] |
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| - | '''CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END''' | + | {{Structure |
| + | |PDB= 1dvl |SIZE=350|CAPTION= <scene name='initialview01'>1dvl</scene>, resolution 2.4Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=NT:NETROPSIN'>NT</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1DVL is a [ | + | 1DVL is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVL OCA]. |
==Reference== | ==Reference== | ||
| - | Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin., Shi K, Mitra SN, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):601-6. Epub 2002, Mar 22. PMID:[http:// | + | Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin., Shi K, Mitra SN, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):601-6. Epub 2002, Mar 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11914483 11914483] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Mitra, S N.]] | [[Category: Mitra, S N.]] | ||
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[[Category: drug binding]] | [[Category: drug binding]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:45:05 2008'' |
Revision as of 08:45, 20 March 2008
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| , resolution 2.4Å | |||||||
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| Ligands: | |||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END
Overview
The crystal structure of the 1:1 complex of netropsin and the B-DNA decamer d(CCIICICCII)(2) has been elucidated and refined to an R factor of 19.6% and an R(free) of 24.7% using 1790 reflections in the resolution range 8-2.4 A. The complex crystallizes in space group C2, with unit-cell parameters a = 62.40, b = 24.47, c = 36.31 A, beta = 110.09 degrees and one molecule of netropsin in the asymmetric unit; the rest of the minor groove is filled with six water molecules. The structure was solved by the molecular-replacement method using the DNA model d(CCCCCIIIII)(2) from the 2:1 netropsin complex by removing both bound netropsins (Chen et al., 1998). Surprisingly, only one netropsin molecule is found to bind to the present decamer, covering residues 2-6 at the upper stream of the duplex. The positively charged guanidinium head is hydrogen bonded through N1H(2) to the O(2) of cytosine 2 and through N10H(2) to N(3) of inosine 6. The three amide N-H groups of the peptides face the minor groove and form three sets of bifurcated hydrogen bonds with the base atoms. The central part of the drug (C3-N8) is nearly conjugated. The preference of the cytosine carbonyl O2 atoms over the inosine N3 atoms in hydrogen bonding is seen. The drug-bound region has more uniform twists, roll angles, propeller twists and minor-groove widths compared with the water-bound region.
About this Structure
1DVL is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin., Shi K, Mitra SN, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):601-6. Epub 2002, Mar 22. PMID:11914483
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