Research workbench
X-ray crystallographic structure of a giant double-walled peptide nanotube formed by a macrocyclic beta-sheet containing ABETA16-22
Analyse X-ray crystallographic structure of a giant double-walled peptide nanotube… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VF1
- Type
- protein
- Length
- 96 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orn-lys-leu-val-phi-phe-ala-glu-orn-glu-ala-phe-mea-val- leu-lys
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 69% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Orn-lys-leu-val-phi-phe-ala-glu-orn-glu-ala-phe-mea-val- leu-lys | protein | 16 | 0% helix, 69% strand | — |
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 | 322 | 0.64 | 0.79 | 27 | empty |
Interfaces
10 interfaces between chains.
- A–D · 306 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 293 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 208 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 195 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (nonstandard).
Compared structures
- 5VF1 · X-ray Crystallographic Structure of a Giant Double-Walled Peptide Nanotube Formed by a… · 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 5VF1 · PDBe 5VF1
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