Research workbench
The crystal structure of a parallel-stranded parallel- stranded guanine tetraplex at 0.95 ångström resolution
Analyse The crystal structure of a parallel-stranded parallel- stranded guanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 352D
- Type
- DNA
- Length
- 87 nucleotides
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
- Ligands
- NA, CA
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, I, J, L, M, P | DNA (5'-D(*TP*GP*GP*GP*GP*T)-3') | dna | 6 | — | — |
| B, E, H, O | DNA (5'-D(*TP*GP*GP*GP*GP*T)-3') | dna | 5 | — | — |
| C, G, N | DNA (5'-D(*TP*GP*GP*GP*GP*T)-3') | dna | 5 | — | — |
| K | DNA (5'-D(*TP*GP*GP*GP*GP*T)-3') | dna | 4 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- CA · Calcium ion · metal · 9 copies · chains A, D, G, B, F, C, E, K, O, P, J, M, I, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.69 | 0.78 | 41 | CA |
Interfaces
56 interfaces between chains.
- A–D · 359 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- M–N · 358 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- E–F · 308 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- I–L · 272 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- F–G · 264 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Compared structures
- 352D · The crystal structure of a parallel-stranded parallel-stranded guanine tetraplex at 0.95… · 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 352D · PDBe 352D
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