Research workbench
DNA containing CU(II)-mediated 4-N-carboxymethylcytosine base pairs
Analyse DNA containing CU(II)-mediated 4-N-carboxymethylcytosine base pairs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EAY
- Type
- DNA
- Length
- 144 nucleotides
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
- Ligands
- NCO, CU, K, CO
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 17 copies · chains A, B, G, C, D, E, F, H, I, J, K, L
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- K · Potassium ion · metal · 4 copies · chains A, C, E, G, H, I, K
- CO · Cobalt (II) ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.55 | 0.78 | 18 | NCO |
| 2 | 226 | 0.53 | 0.77 | 17 | NCO |
| 3 | 231 | 0.52 | 0.77 | 18 | NCO |
Interfaces
27 interfaces between chains.
- E–F · 396 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- I–J · 396 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- C–D · 393 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- G–H · 392 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–B · 391 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 24 modified (nucleotide modification).
Compared structures
- 7EAY · DNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7EAY · PDBe 7EAY
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