Research workbench
Cross-alpha amyloid-like structure alphaaml, 2ND form
Analyse Cross-alpha amyloid-like structure alphaaml, 2ND form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D02
- Type
- protein
- Length
- 777 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amyloid peptide alphaaml
- Ligands
- NH2, PO4, CO3
- Pockets
- 19 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, J, K, M, O, Q, R, T, Z, d | Alpha-amyloid peptide alphaaml | protein | 25 | 88% helix, 0% strand | — |
| B, C, D, G, H, I, L, N, P, S, U, V, W, X, Y, a, e | Alpha-amyloid peptide alphaaml | protein | 24 | 75% helix, 0% strand | — |
| b, f | Alpha-amyloid peptide alphaaml | protein | 23 | 91% helix, 0% strand | — |
| c | Alpha-amyloid peptide alphaaml | protein | 23 | 87% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 11 copies · chains A, E, D, F, J, K, U, C, M, O, Y, G, Q, R, T, b, d
- PO4 · Phosphate ion · ion · 3 copies · chains C, E, G, I, K, M
- CO3 · Carbonate ion · ion · chains O, Q, S, U
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.65 | 0.77 | 53 | empty |
| 2 | 353 | 0.64 | 0.79 | 48 | CO3 |
| 3 | 50 | 0.53 | 0.88 | 12 | empty |
| 4 | 157 | 0.52 | 0.79 | 29 | empty |
| 5 | 63 | 0.51 | 0.85 | 17 | empty |
Interfaces
83 interfaces between chains.
- I–K · 585 Ų buried · 4 hydrogen bonds · protein-protein
- Q–S · 572 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 538 Ų buried · 3 hydrogen bonds · protein-protein
- U–W · 538 Ų buried · 2 hydrogen bonds · protein-protein
- c–d · 501 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6D02 · Cross-alpha Amyloid-like Structure alphaAmL, 2nd form · the same entry in another collection · chain B against B, 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 6D02 · PDBe 6D02
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