Research workbench
U shaped head to head four-way junction in D(TTCTGCTGCTGAA/TTCTGCAGCTGAA) sequence
Analyse U shaped head to head four-way junction in D(TTCTGCTGCTGAA/TTCTGCAGCTGAA)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M5J
- Type
- DNA
- Length
- 52 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3'); DNA…
- Ligands
- F1R, CO
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | DNA (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3') | dna | 13 | — | — |
| B | DNA (5'-D(P*TP*TP*CP*TP*GP*CP*AP*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 | 135 | 0.37 | 0.73 | 11 | F1R |
| 2 | 117 | 0.34 | 0.73 | 9 | F1R, CO |
| 3 | 86 | 0.29 | 0.72 | 10 | F1R |
| 4 | 70 | 0.26 | 0.72 | 8 | F1R |
Interfaces
6 interfaces between chains.
- A–C · 447 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- B–D · 433 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- A–D · 355 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–C · 355 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- A–B · 242 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
- 6M5J · U shaped head to head four-way junction in d(TTCTGCTGCTGAA/TTCTGCAGCTGAA) 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 6M5J · PDBe 6M5J
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