Research workbench
Crystal structure of color device state B
Analyse Crystal structure of color device state B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I6Q
- Type
- DNA
- Length
- 136 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*TP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)- 3'); DNA…
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 8 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*GP*TP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)- 3') | dna | 21 | — | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3') | dna | 14 | — | — |
| D | DNA (5'-D(*AP*CP*AP*GP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3') | dna | 14 | — | — |
| E | DNA (5'-D(*TP*GP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3') | dna | 14 | — | — |
| F | DNA (5'- D(*CP*AP*GP*AP*TP*AP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*TP*AP*CP*G)- 3') | dna | 21 | — | — |
| G | DNA (5'- D(*GP*AP*GP*CP*GP*AP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)- 3') | dna | 21 | — | — |
| H | DNA (5'-D(P*TP*AP*GP*AP*C)-3') | dna | 5 | — | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.48 | 0.72 | 27 | empty |
| 2 | 245 | 0.44 | 0.72 | 18 | empty |
| 3 | 174 | 0.40 | 0.73 | 18 | empty |
Interfaces
13 interfaces between chains.
- A–B · 360 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- E–G · 339 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- B–F · 339 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- B–G · 337 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- A–C · 323 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 5I6Q · Crystal structure of color device state B · 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 5I6Q · PDBe 5I6Q
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