Research workbench
Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant
Analyse Dioxane contributes to the altered conformation and oligomerization state of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y66
- Type
- protein
- Length
- 186 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engrailed homeodomain
- Ligands
- CD
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Engrailed homeodomain | protein | 50 | 92% helix, 0% strand | — |
| B, D | Engrailed homeodomain | protein | 46 | 89% helix, 0% strand | — |
| C | Engrailed homeodomain | protein | 44 | 89% helix, 0% strand | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains A, B, C, D
- DIO · 1,4-diethylene dioxide · additive · 10 copies · chains B, C, A, D
- ACY · Acetic acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.74 | 0.94 | 16 | DIO |
| 2 | 252 | 0.63 | 0.81 | 23 | DIO |
| 3 | 82 | 0.49 | 0.82 | 15 | empty |
| 4 | 74 | 0.36 | 0.77 | 14 | empty |
| 5 | 56 | 0.31 | 0.76 | 14 | DIO |
Interfaces
6 interfaces between chains.
- A–B · 1120 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1052 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 645 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 330 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1Y66 · Dioxane contributes to the altered conformation and oligomerization state of a designed… · 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 1Y66 · PDBe 1Y66
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