Research workbench
X-ray crystal structure of a de novo selected helix-loop-helix heterodimer in a syn arrangement, 26alpha/26beta
Analyse X-ray crystal structure of a de novo selected helix-loop-helix heterodimer in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BCT
- Type
- protein
- Length
- 389 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Molecule
- 26alpha; 26beta
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.7 · 4 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, H | 26alpha | protein | 49 | 82% helix, 0% strand | — |
| G, E | 26beta | protein | 48 | 81% helix, 0% strand | — |
| A, C | 26beta | protein | 49 | 80% helix, 0% strand | — |
| F | 26alpha | protein | 48 | 81% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains D, G, B, E, C, F
- GOL · Glycerol · additive · 4 copies · chains D, F, B, A, E, C
- ACT · Acetate ion · additive · 4 copies · chains G, E, B, A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.72 | 0.79 | 64 | GOL, SO4, ACT |
| 2 | 175 | 0.60 | 0.82 | 19 | SO4 |
| 3 | 75 | 0.38 | 0.78 | 15 | empty |
| 4 | 54 | 0.27 | 0.74 | 11 | empty |
Interfaces
16 interfaces between chains.
- D–C · 1093 Ų buried · 2 hydrogen bonds · protein-protein
- B–A · 1083 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 1046 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 962 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 466 Ų buried · 6 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8BCT · PDBe 8BCT
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