MolNFT v1 · #118684 · DNA
Crystal structure of rich-at DNA 20MER
5F9I · DNA (5'- D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*…: “Crystal structure of rich-at DNA 20MER”. X-ray diffraction, 4 pockets (best druggability 0.42). MolNFT v1 #118684 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5F9I
- Type
- DNA
- Length
- 80 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'- D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3') | dna | 20 | — | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.42 | 0.77 | 14 | empty |
| 2 | 162 | 0.40 | 0.74 | 22 | empty |
| 3 | 112 | 0.36 | 0.74 | 16 | empty |
| 4 | 70 | 0.28 | 0.73 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 900 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- C–D · 884 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- B–D · 82 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–D · 30 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 5F9I · Crystal Structure of rich-AT DNA 20mer · 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 5F9I · PDBe 5F9I
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