Research workbench
Structure of pyroglutamate-abeta-specific Fab C#17 in complex with human abeta-PE3-12PEGB
Analyse Structure of pyroglutamate-abeta-specific Fab C#17 in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MY4
- Type
- protein
- Length
- 441 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; Pyroglutamate-abeta PE3-12-pegb
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab C#17 light chain | protein | 218 | 6% helix, 51% strand | — |
| B | Fab C#17 heavy chain | protein | 217 | 7% helix, 56% strand | — |
| C | Pyroglutamate-abeta PE3-12-pegb | protein | 6 | 0% helix, 33% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.51 | 0.74 | 42 | empty |
| 2 | 58 | 0.50 | 0.86 | 19 | empty |
| 3 | 120 | 0.41 | 0.76 | 24 | empty |
| 4 | 63 | 0.30 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1793 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 150 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5MY4 · Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex with human Abeta-pE3-12PEGb · the same entry in another collection · chain A against A, 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 5MY4 · PDBe 5MY4
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