MolNFT v1 · #153963 · protein + DNA
Universal rvd R* accommodates 5MC via water-mediated interactions
6JW1 · Tal effector: “Universal rvd R* accommodates 5MC via water-mediated interactions”. X-ray diffraction, 7 pockets (best druggability 0.79). MolNFT v1 #153963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JW1
- 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*(5CM) P*GP*CP*GP*TP*CP*TP*CP*T)-3'); DNA…
- Pockets
- 7 · best druggability 0.79
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*(5CM) P*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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.79 | 0.81 | 111 | empty |
| 2 | 1064 | 0.78 | 0.80 | 107 | empty |
| 3 | 224 | 0.56 | 0.78 | 30 | empty |
| 4 | 207 | 0.41 | 0.72 | 20 | empty |
| 5 | 56 | 0.38 | 0.79 | 15 | empty |
Interfaces
11 interfaces between chains.
- A–I · 1803 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 1685 Ų buried · 29 hydrogen bonds · protein-nucleic
- I–J · 749 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- C–D · 721 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–B · 692 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6JW1 · Universal RVD R* accommodates 5mC 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 6JW1 · PDBe 6JW1
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