MolNFT v1 · #127518 · protein
Structure of pyroglutamate-abeta-specific Fab C#24 in complex with human abeta-PE3-18
5MYX · Fab C#24 light chain: “Structure of pyroglutamate-abeta-specific Fab C#24 in complex with human abeta-PE3-18”. X-ray diffraction, 9 pockets (best druggability 0.71). MolNFT v1 #127518 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MYX
- Type
- protein
- Length
- 890 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab C#24 light chain; Fab C#24 heavy chain; Pyroglutamate-abeta PE3-18
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab C#24 light chain | protein | 219 | 7% helix, 52% strand | — |
| B | Fab C#24 heavy chain | protein | 217 | 8% helix, 50% strand | — |
| C | Fab C#24 light chain | protein | 218 | 6% helix, 52% strand | — |
| D | Fab C#24 heavy chain | protein | 208 | 6% helix, 53% strand | — |
| E | Pyroglutamate-abeta PE3-18 | protein | 12 | 0% helix, 0% strand | — |
| F | Pyroglutamate-abeta PE3-18 | protein | 16 | 19% helix, 6% strand | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.71 | 0.77 | 73 | empty |
| 2 | 1058 | 0.69 | 0.74 | 101 | empty |
| 3 | 664 | 0.66 | 0.76 | 49 | empty |
| 4 | 629 | 0.63 | 0.74 | 58 | empty |
| 5 | 207 | 0.52 | 0.77 | 28 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1821 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1668 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 625 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 526 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 482 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 modified (disulfide, cyclization).
Compared structures
- 5MYX · Structure of Pyroglutamate-Abeta-specific Fab c#24 in complex with human Abeta-pE3-18 · 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 5MYX · PDBe 5MYX
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