Research workbench
Amyloid fibril from the antimicrobial peptide uperin 3.5
Analyse Amyloid fibril from the antimicrobial peptide uperin 3.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QV5
- Type
- protein
- Length
- 342 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uperin-3.5
- UniProt
- P82042
- Ligands
- NH2
- Pockets
- 4 · best druggability 0.51
Structure
electron microscopy · 3 distinct chains · 0% helix, 76% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V, Y | Uperin-3.5 | protein | 17 | 0% helix, 76% strand | P82042 |
| B, E, H, K, N, Q, T, W, Z | Uperin-3.5 | protein | 14 | 0% helix, 79% strand | P82042 |
| C, F, I, L, O, R, U, X, a | Uperin-3.5 | protein | 7 | 0% helix, 71% strand | P82042 |
Ligands and binding sites
- NH2 · Amino group · ion · 18 copies · chains A, C, L, B, D, M, F, O, E, G, P, I, R, H, J, U, K, V, X, N, Y, a, Q, S, T, W, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.51 | 0.80 | 18 | empty |
| 2 | 82 | 0.37 | 0.76 | 12 | empty |
| 3 | 73 | 0.35 | 0.76 | 12 | empty |
| 4 | 64 | 0.35 | 0.77 | 12 | empty |
Interfaces
105 interfaces between chains.
- P–Y · 706 Ų buried · 21 hydrogen bonds · protein-protein
- G–P · 705 Ų buried · 21 hydrogen bonds · protein-protein
- A–J · 703 Ų buried · 21 hydrogen bonds · protein-protein
- J–S · 703 Ų buried · 21 hydrogen bonds · protein-protein
- M–V · 698 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7QV5 · Amyloid fibril from the antimicrobial peptide uperin 3.5 · the same entry in another collection · chain J against J, 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
- Every structure of UniProt P82042
- Elsewhere: RCSB PDB 7QV5 · PDBe 7QV5 · UniProt P82042
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