Research workbench
Amyloid fibril morphology II (in vitro) from murine SAA1.1 protein
Analyse Amyloid fibril morphology II (in vitro) from murine SAA1.1 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZCG
- Type
- protein
- Length
- 888 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum amyloid a-2 protein
- UniProt
- P05367
- Pockets
- 9 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 0% helix, 84% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, O, I, N, H, K, E, J, D, G, A, F, C, B, P, S, M, R, T, W, Q, V, X, U | Serum amyloid a-2 protein | protein | 37 | 0% helix, 84% strand | P05367 |
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.77 | 0.89 | 30 | empty |
| 2 | 252 | 0.76 | 0.89 | 30 | empty |
| 3 | 171 | 0.73 | 0.91 | 36 | empty |
| 4 | 177 | 0.69 | 0.88 | 36 | empty |
| 5 | 587 | 0.63 | 0.75 | 40 | empty |
Interfaces
90 interfaces between chains.
- L–P · 1596 Ų buried · 53 hydrogen bonds · protein-protein
- P–T · 1593 Ų buried · 53 hydrogen bonds · protein-protein
- L–H · 1593 Ų buried · 53 hydrogen bonds · protein-protein
- N–J · 1591 Ų buried · 50 hydrogen bonds · protein-protein
- T–X · 1591 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 6ZCG · Amyloid fibril morphology ii (in vitro) from murine SAA1.1 protein · the same entry in another collection · chain L against L, 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 P05367
- Elsewhere: RCSB PDB 6ZCG · PDBe 6ZCG · UniProt P05367
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