Research workbench
Structure of octameric left-handed 310-helix bundle: D-310HD
Analyse Structure of octameric left-handed 310-helix bundle: D-310HD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QDI
- Type
- protein
- Length
- 238 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-310HD
- Ligands
- SO4, BO3
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 91% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-310HD | protein | 31 | 87% helix, 0% strand | — |
| B | D-310HD | protein | 30 | 90% helix, 0% strand | — |
| C, E, G | D-310HD | protein | 30 | 93% helix, 0% strand | — |
| D, F, H | D-310HD | protein | 29 | 93% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, H, C, D, E
- BO3 · Boric acid · ion · 2 copies · chains C, D, E
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D, E, F, H, G
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C, E, F, G
- PGE · Triethylene glycol · additive · 2 copies · chains A, H, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A, B, C
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains C, D, E
- PG4 · Tetraethylene glycol · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.73 | 0.86 | 27 | EDO |
Interfaces
14 interfaces between chains.
- A–B · 981 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 953 Ų buried · 1 hydrogen bond · protein-protein
- F–G · 899 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 891 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 871 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 136 d-amino, 96 modified (D-amino acid, nonstandard).
Compared structures
- 7QDI · Structure of octameric left-handed 310-helix bundle: D-310HD · the same entry in another collection · chain E against E, 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 7QDI · PDBe 7QDI
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