Research workbench
The high-resolution crystal structure of a parallel- stranded guanine tetraplex
Analyse The high-resolution crystal structure of a parallel- stranded guanine tetraplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 244D
- Type
- DNA
- Length
- 91 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
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, G, H, I, J, L, M, N, P | DNA (5'-D(*TP*GP*GP*GP*GP*T)-3') | dna | 6 | — | — |
| B, E, K, O | DNA (5'-D(*TP*GP*GP*GP*GP*T)-3') | dna | 5 | — | — |
| C | DNA (5'-D(*TP*GP*GP*GP*GP*T)-3') | dna | 5 | — | — |
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, H, L, N, O, J, M, P, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.67 | 0.78 | 33 | CA |
| 2 | 75 | 0.30 | 0.74 | 13 | empty |
| 3 | 55 | 0.27 | 0.74 | 10 | CA |
Interfaces
55 interfaces between chains.
- M–N · 354 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- A–D · 353 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- E–F · 304 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- B–C · 267 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- I–L · 266 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Compared structures
- 244D · The high-resolution crystal structure of a parallel-stranded guanine tetraplex · 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 244D · PDBe 244D
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