MolNFT v1 · #67276 · protein
X-ray structure of amyloid beta PEPTIDE:ANTIBODY (ABETA1-7:12B4) complex
3IFP · 12B4 Fab antibody heavy chain: “X-ray structure of amyloid beta PEPTIDE:ANTIBODY (ABETA1-7:12B4) complex”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #67276 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3IFP
- Type
- protein
- Length
- 1,765 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12B4 Fab antibody heavy chain; 12B4 Fab antibody light chain; Amyloid beta A4 protein
- UniProt
- P05067
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 12B4 Fab antibody heavy chain | protein | 222 | 4% helix, 48% strand | — |
| L, B, D, F | 12B4 Fab antibody light chain | protein | 218 | 6% helix, 52% strand | — |
| P, Q, R | Amyloid beta A4 protein | protein | 6 | 0% helix, 17% strand | P05067 |
| A, C, E | 12B4 Fab antibody heavy chain | protein | 216 | 4% helix, 49% strand | — |
| S | Amyloid beta A4 protein | protein | 5 | 0% helix, 20% strand | P05067 |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.74 | 0.78 | 111 | empty |
| 2 | 814 | 0.72 | 0.77 | 97 | empty |
| 3 | 179 | 0.62 | 0.83 | 22 | empty |
| 4 | 322 | 0.52 | 0.74 | 50 | empty |
| 5 | 253 | 0.49 | 0.74 | 39 | empty |
Interfaces
21 interfaces between chains.
- H–L · 1832 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1781 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1774 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1772 Ų buried · 14 hydrogen bonds · protein-protein
- H–P · 381 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3IFP · X-ray structure of amyloid beta peptide:antibody (Abeta1-7:12B4) complex · the same entry in another collection · chain S against S, 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 3IFP · PDBe 3IFP · UniProt P05067
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