Research workbench
A de novo designed heptameric coiled coil cc-hept-homocys-H-E
Analyse A de novo designed heptameric coiled coil cc-hept-homocys-H-E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F2Y
- Type
- protein
- Length
- 181 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cc-hept-hcys-H-E
- Ligands
- ACE
- Pockets
- 1 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Cc-hept-hcys-H-E | protein | 28 | 89% helix, 0% strand | — |
| B, C, F | Cc-hept-hcys-H-E | protein | 25 | 84% helix, 0% strand | — |
| D | Cc-hept-hcys-H-E | protein | 23 | 78% helix, 0% strand | — |
| E | Cc-hept-hcys-H-E | protein | 27 | 93% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 7 copies · chains A, C, B, G, D, 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 | 762 | 0.84 | 0.86 | 58 | empty |
Interfaces
9 interfaces between chains.
- A–F · 733 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 730 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 694 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 620 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent, 7 modified (covalent ligand, nonstandard).
Compared structures
- 5F2Y · A de novo designed heptameric coiled coil CC-Hept-homoCys-H-E · 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 5F2Y · PDBe 5F2Y
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