Research workbench
Vhs domain of human GGA1 complexed with sotilin C-terminal peptide
Analyse Vhs domain of human GGA1 complexed with sotilin C-terminal peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G2U
- Type
- protein
- Length
- 294 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 0.75
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor-binding protein GGA1 | protein | 140 | 71% helix, 0% strand | Q9UJY5 |
| C, 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 | 538 | 0.75 | 0.83 | 60 | empty |
| 2 | 80 | 0.47 | 0.82 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 664 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 481 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3G2U · VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide · the same entry in another collection · chain A against A, 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
- Q99523 · AlphaFold monomer V2.0 prediction for sortilin (Q99523) · a predicted model of the same protein · chain C against A, TM-score 0.56
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 3G2U · PDBe 3G2U · UniProt Q9UJY5 · UniProt Q99523
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