Research workbench
GGA3 vhs domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor
Analyse GGA3 vhs domain complexed with C-terminal peptide from cation-independent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JPL
- Type
- protein
- Length
- 673 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor binding protein GGA3; Cation-independent mannose 6-phosphate…
- UniProt
- Q9NZ52, P11717
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ADP-ribosylation factor binding protein GGA3 | protein | 161 | 70% helix, 0% strand | Q9NZ52 |
| E, F, G | Cation-independent mannose 6-phosphate receptor | protein | 8 | 0% helix, 0% strand | P11717 |
| B, C | ADP-ribosylation factor binding protein GGA3 | protein | 159 | 69% helix, 0% strand | Q9NZ52 |
| H | Cation-independent mannose 6-phosphate receptor | protein | 9 | 0% helix, 0% strand | P11717 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.72 | 0.80 | 63 | empty |
| 2 | 464 | 0.68 | 0.79 | 59 | empty |
| 3 | 213 | 0.53 | 0.77 | 31 | empty |
| 4 | 120 | 0.51 | 0.81 | 17 | empty |
| 5 | 161 | 0.47 | 0.76 | 19 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1194 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1183 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 588 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 566 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 562 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1JPL · GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9NZ52 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-binding protein GGA3… · a predicted model of the same protein · chain C against A, TM-score 0.92
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 Q9NZ52
- Every structure of UniProt P11717
- Elsewhere: RCSB PDB 1JPL · PDBe 1JPL · UniProt Q9NZ52 · UniProt P11717
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