Research workbench
Vhs domain of human GGA1 complexed with sotilin C-terminal phosphopeptide
Analyse Vhs domain of human GGA1 complexed with sotilin C-terminal phosphopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G2V
- Type
- protein
- Length
- 296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-binding protein GGA1; C-terminal fragment of sortilin
- UniProt
- Q9UJY5, Q99523
- Ligands
- IOD
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor-binding protein GGA1 | protein | 140 | 70% helix, 0% strand | Q9UJY5 |
| C | C-terminal fragment of sortilin | protein | 9 | 0% helix, 0% strand | Q99523 |
| D | C-terminal fragment of sortilin | protein | 7 | 0% helix, 0% strand | Q99523 |
Ligands and binding sites
- IOD · Iodide ion · ion · 5 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 | 478 | 0.74 | 0.83 | 59 | empty |
| 2 | 89 | 0.46 | 0.81 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 606 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 513 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, phosphorylation).
Compared structures
- 3G2V · VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide · 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 A against A, TM-score 0.99
- Q99523 · AlphaFold monomer V2.0 prediction for sortilin (Q99523) · a predicted model of the same protein · chain D against A, TM-score 0.63
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 Q99523
- Elsewhere: RCSB PDB 3G2V · PDBe 3G2V · UniProt Q9UJY5 · UniProt Q99523
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