MolNFT v1 · #153961 · protein + DNA
Rvd ha specifically contacts 5MC through van der waals interactions
6JVZ · Tal effector: “Rvd ha specifically contacts 5MC through van der waals interactions”. X-ray diffraction, 10 pockets (best druggability 0.80). MolNFT v1 #153961 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JVZ
- Type
- protein + DNA
- Length
- 1,062 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
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tal effector | protein | 497 | 73% 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.80 | 0.82 | 126 | empty |
| 2 | 835 | 0.78 | 0.81 | 83 | empty |
| 3 | 240 | 0.67 | 0.84 | 35 | empty |
| 4 | 315 | 0.63 | 0.80 | 34 | empty |
| 5 | 261 | 0.57 | 0.77 | 35 | empty |
Interfaces
11 interfaces between chains.
- A–I · 1790 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 1774 Ų buried · 25 hydrogen bonds · protein-nucleic
- I–J · 776 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- C–D · 723 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–B · 624 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6JVZ · RVD HA specifically contacts 5mC through van der Waals 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 6JVZ · PDBe 6JVZ
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