Research workbench
Structure of pyroglutamate-abeta-specific Fab C#17 in complex with murine abeta-PE3-18PEGB
Analyse Structure of pyroglutamate-abeta-specific Fab C#17 in complex with murine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MYK
- Type
- protein
- Length
- 443 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab C#17 light chain; Fab C#17 heavy chain; Amyloid beta A4 protein
- UniProt
- P12023
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab C#17 light chain | protein | 219 | 7% helix, 53% strand | — |
| B | Fab C#17 heavy chain | protein | 218 | 7% helix, 55% strand | — |
| C | Amyloid beta A4 protein | protein | 6 | 0% helix, 33% strand | P12023 |
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 | 387 | 0.55 | 0.74 | 49 | empty |
| 2 | 114 | 0.39 | 0.75 | 26 | empty |
| 3 | 78 | 0.36 | 0.77 | 16 | empty |
| 4 | 66 | 0.32 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1896 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5MYK · Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex with murine Abeta-pE3-18PEGb · the same entry in another collection · chain A against A, TM-score 1.00
- P12023 · AlphaFold monomer V2.0 prediction for amyloid-beta A4 protein (P12023) · a predicted model of the same protein · chain C 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 P12023
- Elsewhere: RCSB PDB 5MYK · PDBe 5MYK · UniProt P12023
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