Research workbench
A de novo designed pentameric coiled coil cc-pent.
Analyse A de novo designed pentameric coiled coil cc-pent. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PN8
- Type
- protein
- Length
- 299 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cc-pent
- Ligands
- ACE
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, J | Cc-pent | protein | 30 | 93% helix, 0% strand | — |
| I | Cc-pent | protein | 29 | 93% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.77 | 0.93 | 25 | empty |
| 2 | 134 | 0.77 | 0.93 | 25 | empty |
| 3 | 86 | 0.68 | 0.91 | 20 | empty |
| 4 | 250 | 0.50 | 0.74 | 31 | empty |
| 5 | 159 | 0.41 | 0.74 | 20 | empty |
Interfaces
13 interfaces between chains.
- F–G · 812 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 788 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 785 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 782 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 781 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 4PN8 · A de novo designed pentameric coiled coil CC-Pent. · the same entry in another collection · chain C against C, 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 4PN8 · PDBe 4PN8
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