Research workbench
Structural insights into the quadruplex-duplex 3' interface formed from a telomeric repeat - ttloop
Analyse Structural insights into the quadruplex-duplex 3' interface formed from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DWW
- Type
- DNA
- Length
- 131 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (25-mer); DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
- Ligands
- K
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | DNA (25-mer) | dna | 25 | — | — |
| B, D, H | DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3') | dna | 8 | — | — |
| F | DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3') | dna | 7 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 10 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.63 | 0.76 | 38 | empty |
| 2 | 66 | 0.32 | 0.76 | 10 | empty |
| 3 | 60 | 0.30 | 0.76 | 11 | empty |
| 4 | 53 | 0.25 | 0.74 | 13 | empty |
| 5 | 56 | 0.25 | 0.73 | 12 | empty |
Interfaces
8 interfaces between chains.
- A–B · 559 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- C–D · 534 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- G–H · 526 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- E–F · 525 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- E–G · 467 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 5DWW · Structural Insights into the Quadruplex-Duplex 3' Interface formed from a Telomeric… · the same entry in another collection · chain H against H, 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 5DWW · PDBe 5DWW
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