Research workbench
Universal rvd R* accommodates 5HMC via water-mediated interactions
Analyse Universal rvd R* accommodates 5HMC 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
- 6JW2
- Type
- protein + DNA
- Length
- 2,108 residues
- Chains
- 12
- 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*(5HC) P*GP*CP*GP*TP*CP*TP*CP*T)-3'); DNA…
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, H | Tal effector | protein | 493 | 71% helix, 0% strand | — |
| I, C, F, K | DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC) P*GP*CP*GP*TP*CP*TP*CP*T)-3') | dna | 17 | — | — |
| J, D, G, L | DNA (5'- D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3') | dna | 17 | — | — |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.83 | 0.84 | 126 | empty |
| 2 | 1188 | 0.79 | 0.81 | 111 | empty |
| 3 | 1177 | 0.79 | 0.81 | 124 | empty |
| 4 | 1162 | 0.78 | 0.80 | 119 | empty |
| 5 | 705 | 0.66 | 0.75 | 54 | empty |
Interfaces
20 interfaces between chains.
- E–F · 1719 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 1700 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–I · 1698 Ų buried · 27 hydrogen bonds · protein-nucleic
- H–K · 1688 Ų buried · 26 hydrogen bonds · protein-nucleic
- I–J · 761 Ų buried · 63 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6JW2 · Universal RVD R* accommodates 5hmC 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 6JW2 · PDBe 6JW2
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