Research workbench
A de novo designed coiled coil cc-tri
Analyse A de novo designed coiled coil cc-tri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DZL
- Type
- protein
- Length
- 360 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coiled-coil peptide cc-tri
- Ligands
- ACE
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, J, K | Coiled-coil peptide cc-tri | protein | 30 | 90% helix, 0% strand | — |
| I | Coiled-coil peptide cc-tri | protein | 31 | 90% helix, 0% strand | — |
| C, B, F | Coiled-coil peptide cc-tri | protein | 32 | 84% helix, 0% strand | — |
| E | Coiled-coil peptide cc-tri | protein | 31 | 84% helix, 0% strand | — |
| G | Coiled-coil peptide cc-tri | protein | 28 | 93% helix, 0% strand | — |
| D | Coiled-coil peptide cc-tri | protein | 27 | 93% helix, 0% strand | — |
| L | Coiled-coil peptide cc-tri | protein | 27 | 85% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 7 copies · chains A, I, C, B, F, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.68 | 0.81 | 36 | empty |
| 2 | 257 | 0.55 | 0.77 | 29 | empty |
| 3 | 136 | 0.48 | 0.78 | 18 | empty |
| 4 | 138 | 0.40 | 0.74 | 21 | empty |
| 5 | 50 | 0.37 | 0.80 | 9 | empty |
Interfaces
29 interfaces between chains.
- E–F · 601 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 590 Ų buried · 4 hydrogen bonds · protein-protein
- J–K · 580 Ų buried · 5 hydrogen bonds · protein-protein
- F–D · 573 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 572 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 7 covalent (nonstandard, covalent ligand).
Compared structures
- 4DZL · A de novo designed Coiled Coil CC-Tri · 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 4DZL · PDBe 4DZL
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