5mC interactions in PDB entry 6D1T auto-curated with SNAP
Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.
Summary information and primary citation [schematics · contacts · top · homepage · tutorial]
- PDB-id
- 6D1T
- Class
- DNA binding protein-DNA
- Method
- X-ray (2.25 Å)
- Summary
- Complex of mbd1-mbd and methylated DNA
List of 2 5mC-amino acid contacts:-
B.5CM6: stacking-with-A.ARG22 is-WC-paired is-in-duplex [+]:AcG/cGT
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C.5CM6: stacking-with-A.ARG44 is-WC-paired is-in-duplex [-]:cGT/AcG
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- Reference
- Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium: "Complex of MBD1-MBD and methylated DNA." to be published
- Abstract
Base-block schematics in six views [summary · contacts · top · homepage · tutorial]
- 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.
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List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]
- 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.
