Research workbench
X-ray structure of amyloid beta PEPTIDE:ANTIBODY (ABETA1-7:10D5) complex
Analyse X-ray structure of amyloid beta PEPTIDE:ANTIBODY (ABETA1-7:10D5) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IFO
- Type
- protein
- Length
- 880 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10D5 Fab antibody heavy chain; 10D5 Fab antibody light chain; Amyloid beta A4 protein
- UniProt
- P05067
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | 10D5 Fab antibody heavy chain | protein | 216 | 7% helix, 50% strand | — |
| L, B | 10D5 Fab antibody light chain | protein | 218 | 6% helix, 51% strand | — |
| P, Q | Amyloid beta A4 protein | protein | 6 | 0% helix, 17% strand | P05067 |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.82 | 0.84 | 113 | empty |
| 2 | 186 | 0.48 | 0.76 | 36 | empty |
| 3 | 176 | 0.46 | 0.75 | 21 | empty |
| 4 | 127 | 0.45 | 0.77 | 28 | empty |
| 5 | 68 | 0.41 | 0.80 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1839 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1833 Ų buried · 15 hydrogen bonds · protein-protein
- L–B · 518 Ų buried · 4 hydrogen bonds · protein-protein
- A–Q · 385 Ų buried · 11 hydrogen bonds · protein-protein
- H–P · 358 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3IFO · X-ray structure of amyloid beta peptide:antibody (Abeta1-7:10D5) complex · the same entry in another collection · chain Q against Q, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain P against A, TM-score 0.66
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 3IFO · PDBe 3IFO · UniProt P05067
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