MolNFT v1 · #18724 · protein
Complex of GGA1-vhs domain and beta-secretase C-terminal phosphopeptide
1PY1 · ADP-ribosylation factor binding protein GGA1: “Complex of GGA1-vhs domain and beta-secretase C-terminal phosphopeptide”. X-ray diffraction, 4 pockets (best druggability 0.73). MolNFT v1 #18724 on GenesisL1: 3D structure, binding…
- PDB
- 1PY1
- Type
- protein
- Length
- 588 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor binding protein GGA1; Beta-secretase
- EC
- 3.4.23.-
- UniProt
- Q9UJY5, P56817
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ADP-ribosylation factor binding protein GGA1 | protein | 142 | 70% helix, 0% strand | Q9UJY5 |
| B | ADP-ribosylation factor binding protein GGA1 | protein | 139 | 71% helix, 0% strand | Q9UJY5 |
| C | ADP-ribosylation factor binding protein GGA1 | protein | 138 | 71% helix, 0% strand | Q9UJY5 |
| E, F, H | Beta-secretase (EC 3.4.23.-) | protein | 7 | 0% helix, 0% strand | P56817 |
| G | Beta-secretase (EC 3.4.23.-) | protein | 6 | 0% helix, 0% strand | P56817 |
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 | 550 | 0.73 | 0.81 | 67 | empty |
| 2 | 584 | 0.73 | 0.80 | 58 | empty |
| 3 | 87 | 0.49 | 0.82 | 19 | empty |
| 4 | 88 | 0.47 | 0.82 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 703 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 685 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 492 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 487 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 480 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, phosphorylation).
Compared structures
- 1PY1 · Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide · the same entry in another collection · chain H against H, TM-score 1.00
- Q9UJY5 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-binding protein GGA1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UJY5
- Every structure of UniProt P56817
- Elsewhere: RCSB PDB 1PY1 · PDBe 1PY1 · UniProt Q9UJY5 · UniProt P56817
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