Research workbench
Degenerate rvd rg forms a distinct loop conformation
Analyse Degenerate rvd rg forms a distinct loop conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JW3
- Type
- protein + DNA
- Length
- 2,124 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*(5CM) P*GP*CP*GP*TP*CP*TP*CP*T)-3'); DNA…
- Pockets
- 20 · best druggability 0.80
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 | 497 | 71% helix, 0% strand | — |
| I, C, F, K | DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM) 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
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.80 | 0.82 | 102 | empty |
| 2 | 870 | 0.80 | 0.83 | 91 | empty |
| 3 | 1065 | 0.80 | 0.81 | 105 | empty |
| 4 | 1168 | 0.78 | 0.80 | 120 | empty |
| 5 | 238 | 0.54 | 0.77 | 33 | empty |
Interfaces
20 interfaces between chains.
- E–F · 1707 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 1706 Ų buried · 29 hydrogen bonds · protein-nucleic
- H–K · 1703 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–I · 1693 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–E · 805 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6JW3 · Degenerate RVD RG forms a distinct loop conformation · 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 6JW3 · PDBe 6JW3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.