MolNFT v1 · #127509 · protein
Structure of pyroglutamate-abeta-specific Fab C#6 in complex with human abeta-PE3-12-pegb
5MYO · Fab C#6 light chain: “Structure of pyroglutamate-abeta-specific Fab C#6 in complex with human abeta-PE3-12-pegb”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.74). MolNFT v1 #127509 on GenesisL1: 3D structure…
- PDB
- 5MYO
- Type
- protein
- Length
- 888 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab C#6 light chain; Fab C#6 heavy chain; Amyloid beta A4 protein
- UniProt
- P05067
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab C#6 light chain | protein | 219 | 6% helix, 52% strand | — |
| B | Fab C#6 heavy chain | protein | 221 | 10% helix, 49% strand | — |
| D | Fab C#6 heavy chain | protein | 219 | 7% helix, 51% strand | — |
| E | Amyloid beta A4 protein | protein | 10 | 0% helix, 0% strand | P05067 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.74 | 0.79 | 86 | empty |
| 2 | 372 | 0.74 | 0.85 | 33 | empty |
| 3 | 612 | 0.63 | 0.74 | 65 | empty |
| 4 | 62 | 0.51 | 0.87 | 23 | GOL |
| 5 | 132 | 0.46 | 0.78 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1930 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1783 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 503 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 409 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 399 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5MYO · Structure of Pyroglutamate-Abeta-specific Fab c#6 in complex with human Abeta-pE3-12-PEGb · the same entry in another collection · chain A against A, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain E against A, TM-score 0.36
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 5MYO · PDBe 5MYO · UniProt P05067
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