MolNFT v1 · #93977 · protein
Crystal structure of a humanised 3D6 Fab bound to amyloid beta peptide
4HIX · Humanized 3D6 Fab heavy chain: “Crystal structure of a humanised 3D6 Fab bound to amyloid beta peptide”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1 #93977 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4HIX
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Humanized 3D6 Fab heavy chain; Humanized 3D6 Fab light chain; Beta-amyloid protein 40
- UniProt
- P05067
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Humanized 3D6 Fab heavy chain | protein | 219 | 10% helix, 52% strand | — |
| L | Humanized 3D6 Fab light chain | protein | 219 | 5% helix, 50% strand | — |
| A | Beta-amyloid protein 40 | protein | 6 | 50% helix, 0% strand | P05067 |
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 | 634 | 0.64 | 0.75 | 55 | empty |
| 2 | 100 | 0.39 | 0.76 | 19 | empty |
| 3 | 82 | 0.31 | 0.73 | 19 | empty |
| 4 | 70 | 0.30 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1705 Ų buried · 17 hydrogen bonds · protein-protein
- H–A · 346 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 311 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HIX · Crystal structure of a humanised 3D6 Fab bound to amyloid beta peptide · the same entry in another collection · chain H against H, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain A against A, TM-score 0.70
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 4HIX · PDBe 4HIX · UniProt P05067
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