Research workbench
Structural model for a 40-residue beta-amyloid fibril with three-fold symmetry, negative stagger
Analyse Structural model for a 40-residue beta-amyloid fibril with three-fold symmetry… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2LMQ
- Type
- protein
- Length
- 576 residues
- Chains
- 18
- Method
- solid-state nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-amyloid protein 40
- UniProt
- P05067
- Pockets
- 13 · best druggability 0.78
Structure
solid-state nmr · 1 distinct chain · 0% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R | Beta-amyloid protein 40 | protein | 32 | 0% helix, 38% strand | P05067 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.78 | 0.90 | 60 | empty |
| 2 | 258 | 0.74 | 0.87 | 45 | empty |
| 3 | 222 | 0.72 | 0.88 | 52 | empty |
| 4 | 666 | 0.72 | 0.79 | 55 | empty |
| 5 | 564 | 0.70 | 0.79 | 58 | empty |
Interfaces
88 interfaces between chains.
- K–L · 1413 Ų buried · 36 hydrogen bonds · protein-protein
- O–P · 1397 Ų buried · 28 hydrogen bonds · protein-protein
- I–J · 1395 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1385 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1377 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 2LMQ · Structural Model for a 40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative… · the same entry in another collection · chain K against K, 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 P05067
- Elsewhere: RCSB PDB 2LMQ · PDBe 2LMQ · UniProt P05067
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