Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>.
The block schematics were created with DSSR and
rendered using PyMOL.
- PDB-id
- 5EMC
- Class
- transcription-DNA
- Method
- X-ray (2.3 Å)
- Summary
- Transcription factor grdbd and smgre complex
List of 1 5mC-amino acid contact:
-
D.5CM33: other-contacts is-WC-paired is-in-duplex [-]:TGT/AcA
direct SNAP output · DNAproDB 2.0
- Reference
- Jin, J., Lian, T., SU, X.D.: "The effects of cytosine methylation on general transcription factors." To Be Published
- Abstract
-
- The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model,
with the methyl-carbon atom in black.
- Watson-Crick base pairs are represented as long rectangular blocks with the
minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
- Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code
by chain identifier.
- The block schematics were created with 3DNA-DSSR,
and images were rendered using PyMOL.
- Download the PyMOL session file corresponding to the top-left
image in the following panel.
- The contacts include paired nucleotides (mostly a G in G-C pairing), and
amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
- The structure is oriented in the 'standard' base reference frame of 5mC, allowing for easy comparison
and direct superimposition between entries.
- The black sphere (•) denotes the 5-methyl carbon atom in 5mC.
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No. 1 D.5CM33: download PDB file
for the 5mC entry
other-contacts is-WC-paired is-in-duplex [-]:TGT/AcA
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