Research workbench
Crystal structure of the human FE65-PTB1 domain with bound phosphate (trigonal crystal form)
Analyse Crystal structure of the human FE65-PTB1 domain with bound phosphate (trigonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D8F
- Type
- protein
- Length
- 505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid beta A4 precursor protein-binding family B member 1
- UniProt
- O00213
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Amyloid beta A4 precursor protein-binding family B member 1 | protein | 127 | 26% helix, 41% strand | O00213 |
| B | Amyloid beta A4 precursor protein-binding family B member 1 | protein | 126 | 21% helix, 38% strand | O00213 |
| D | Amyloid beta A4 precursor protein-binding family B member 1 | protein | 125 | 23% helix, 38% strand | O00213 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.73 | 0.78 | 73 | empty |
| 2 | 360 | 0.67 | 0.81 | 36 | empty |
Interfaces
4 interfaces between chains.
- C–D · 694 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 658 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 182 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3D8F · Crystal structure of the human Fe65-PTB1 domain with bound phosphate (trigonal crystal… · the same entry in another collection · chain D against D, TM-score 1.00
- O00213 · AlphaFold monomer V2.0 prediction for amyloid-beta A4 precursor protein-binding family B… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O00213
- Elsewhere: RCSB PDB 3D8F · PDBe 3D8F · UniProt O00213
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