MolNFT v1 · #13224 · protein
Octameric de novo designed peptide
1L4X · Sin-asp-glu-leu-glu-arg-ala-ile-arg-glu-leu-ala-ala-arg…: “Octameric de novo designed peptide”. X-ray diffraction, 3 ligands (MG, NH2, CL), 1 pocket (best druggability 0.87). MolNFT v1 #13224 on GenesisL1: 3D structure, binding…
- PDB
- 1L4X
- Type
- protein
- Length
- 120 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sin-asp-glu-leu-glu-arg-ala-ile-arg-glu-leu-ala-ala-arg- ile-lys-NH2
- Ligands
- MG, NH2, CL
- Pockets
- 1 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Sin-asp-glu-leu-glu-arg-ala-ile-arg-glu-leu-ala-ala-arg- ile-lys-NH2 | protein | 15 | 87% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains G, H
- NH2 · Amino group · ion · 8 copies · chains A, E, B, C, D, F, G, H
- CL · Chloride ion · ion · chains F, G
- SIN · Succinic acid · additive · 8 copies · chains A, B, C, D, F, E, G, H
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 | 281 | 0.87 | 0.97 | 28 | empty |
Interfaces
20 interfaces between chains.
- B–C · 381 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 374 Ų buried · 1 hydrogen bond · protein-protein
- G–H · 374 Ų buried · 1 hydrogen bond · protein-protein
- F–G · 369 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 365 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 covalent (additive adduct).
Compared structures
- 1L4X · Octameric de novo designed peptide · 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 1L4X · PDBe 1L4X
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