MolNFT v1 · #103662 · protein
A de novo designed pentameric coiled coil cc-PENT_VARIANT
4PND: “A de novo designed pentameric coiled coil cc-PENT_VARIANT”. X-ray diffraction, 1 ligand (ACE), 2 pockets (best druggability 0.71). MolNFT v1 #103662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PND
- Type
- protein
- Length
- 149 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cc-PENT_VARIANT
- Ligands
- ACE
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Cc-PENT_VARIANT | protein | 30 | 90% helix, 0% strand | — |
| B | Cc-PENT_VARIANT | protein | 29 | 93% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.71 | 0.87 | 32 | empty |
| 2 | 89 | 0.67 | 0.90 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 759 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 737 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 686 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 659 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4PND · A de novo designed pentameric coiled coil CC-Pent_Variant · 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 4PND · PDBe 4PND
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.