Research workbench
A conformational transition in the structure of a 2'-thiomethyl- modified DNA visualized at high resolution
Analyse A conformational transition in the structure of a 2'-thiomethyl- modified DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EY3
- Type
- DNA
- Length
- 48 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'
- Ligands
- SR
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- SR · Strontium ion · metal · 7 copies · chains B, A, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–B · 634 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–D · 630 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 15 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 3EY3 · A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized… · 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 3EY3 · PDBe 3EY3
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