MolNFT v1 · #177076 · protein
Fab-amyloid beta fragment complex
7E6P · Fab heavy chain: “Fab-amyloid beta fragment complex”. X-ray diffraction, 4 pockets (best druggability 0.53). MolNFT v1 #177076 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E6P
- Type
- protein
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Amyloid beta fragment with an intramolecular disulfide…
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab heavy chain | protein | 218 | 5% helix, 50% strand | — |
| H | Fab light chain | protein | 217 | 10% helix, 54% strand | — |
| A | Amyloid beta fragment with an intramolecular disulfide bond at positions 17 and 28 | protein | 14 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains L, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains L, H
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 | 303 | 0.53 | 0.75 | 41 | EDO |
| 2 | 133 | 0.42 | 0.75 | 22 | PEG |
| 3 | 99 | 0.38 | 0.75 | 18 | empty |
| 4 | 67 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1781 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 463 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 263 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7E6P · Fab-amyloid beta fragment complex · 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
- Elsewhere: RCSB PDB 7E6P · PDBe 7E6P
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