Research workbench
Vhs domain of human GGA1 complexed with C-terminal phosphopeptide from bace
Analyse Vhs domain of human GGA1 complexed with C-terminal phosphopeptide from bace in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UJK
- Type
- protein
- Length
- 299 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor binding protein GGA1; C-terminal peptide from beta-secretase
- EC
- 3.4.23.-
- UniProt
- Q9UJY5, P56817
- Ligands
- IOD
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor binding protein GGA1 | protein | 145 | 69% helix, 0% strand | Q9UJY5 |
| B | ADP-ribosylation factor binding protein GGA1 | protein | 140 | 72% helix, 0% strand | Q9UJY5 |
| C, D | C-terminal peptide from beta-secretase (EC 3.4.23.-) | protein | 7 | 0% helix, 0% strand | P56817 |
Ligands and binding sites
- IOD · Iodide ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.50 | 0.77 | 21 | empty |
| 2 | 122 | 0.39 | 0.75 | 21 | IOD |
Interfaces
3 interfaces between chains.
- A–C · 496 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 485 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 483 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, phosphorylation).
Compared structures
- 1UJK · VHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.99
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain C against A, TM-score 0.50
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 1UJK · PDBe 1UJK · UniProt Q9UJY5 · UniProt P56817
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