Research workbench
Universal rvd R* accommodates cytosine via water-mediated interactions
Analyse Universal rvd R* accommodates cytosine via water-mediated interactions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JW0
- Type
- protein + DNA
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tal effector; DNA (5'- D(*TP*GP*TP*CP*CP*CP*TP*TP*CP*GP*CP*GP*TP*CP*TP*CP*T)-3'); DNA…
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tal effector | protein | 496 | 74% helix, 0% strand | — |
| I, C | DNA (5'- D(*TP*GP*TP*CP*CP*CP*TP*TP*CP*GP*CP*GP*TP*CP*TP*CP*T)-3') | dna | 17 | — | — |
| J, D | DNA (5'- D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3') | dna | 17 | — | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.80 | 0.82 | 126 | empty |
| 2 | 1086 | 0.79 | 0.81 | 114 | empty |
| 3 | 219 | 0.41 | 0.72 | 25 | empty |
| 4 | 54 | 0.36 | 0.79 | 12 | empty |
| 5 | 108 | 0.33 | 0.72 | 19 | empty |
Interfaces
11 interfaces between chains.
- B–C · 1759 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–I · 1744 Ų buried · 25 hydrogen bonds · protein-nucleic
- I–J · 761 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- C–D · 745 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- A–B · 723 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6JW0 · Universal RVD R* accommodates cytosine via water-mediated interactions · 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 6JW0 · PDBe 6JW0
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