Research workbench
U shaped head to head four-way junction in D(TTCTGCTGCTGAA) sequence
Analyse U shaped head to head four-way junction in D(TTCTGCTGCTGAA) sequence in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M4T
- Type
- DNA
- Length
- 52 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*(UD)P*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3')
- Ligands
- F1R, CO
- Pockets
- 4 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'-D(P*(UD)P*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
- F1R · N4-[4-[(6-chloranyl-2-methoxy-acridin-9-yl) amino]butyl]-1,3,5-triazine-2,4,6-triamine · ligand · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 116 | 0.34 | 0.73 | 9 | F1R |
| 2 | 106 | 0.32 | 0.72 | 9 | F1R |
| 3 | 82 | 0.28 | 0.72 | 8 | F1R |
| 4 | 79 | 0.27 | 0.72 | 8 | F1R |
Interfaces
6 interfaces between chains.
- B–D · 433 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- A–C · 429 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- B–C · 359 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–D · 357 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- A–B · 237 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6M4T · U shaped head to head four-way junction in d(TTCTGCTGCTGAA) sequence · 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 6M4T · PDBe 6M4T
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