Research workbench
Structure of the trichomonas vaginalis MYB3 DNA-binding domain bound to a promoter sequence reveals a unique C- terminal beta-hairpin conformation
Analyse Structure of the trichomonas vaginalis MYB3 DNA-binding domain bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZQC
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MYB3; Mre-1
- UniProt
- A2D9X4
- Pockets
- 15 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | MYB3 | protein | 118 | 53% helix, 0% strand | A2D9X4 |
| B, E, H, K | Mre-1 | dna | 16 | — | — |
| C, F, I, L | Mre-1 | dna | 16 | — | — |
| J | MYB3 | protein | 119 | 55% helix, 5% strand | A2D9X4 |
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.65 | 0.77 | 54 | empty |
| 2 | 430 | 0.60 | 0.76 | 48 | empty |
| 3 | 341 | 0.58 | 0.76 | 38 | empty |
| 4 | 231 | 0.55 | 0.78 | 35 | empty |
| 5 | 102 | 0.49 | 0.81 | 16 | empty |
Interfaces
17 interfaces between chains.
- B–C · 727 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- E–F · 724 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- H–I · 713 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- K–L · 710 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–B · 617 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 3ZQC · Structure of the Trichomonas vaginalis Myb3 DNA-binding domain bound to a promoter… · 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
- Every structure of UniProt A2D9X4
- Elsewhere: RCSB PDB 3ZQC · PDBe 3ZQC · UniProt A2D9X4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.