Research workbench
Garp-snare interaction
Analyse Garp-snare interaction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J2C
- Type
- protein
- Length
- 238 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntaxin-6; Vacuolar protein sorting-associated protein 51 homolog
- UniProt
- O43752, Q9UID3
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syntaxin-6 | protein | 108 | 84% helix, 0% strand | O43752 |
| B, D | Vacuolar protein sorting-associated protein 51 homolog | protein | 12 | 67% helix, 0% strand | Q9UID3 |
| C | Syntaxin-6 | protein | 106 | 87% helix, 0% strand | O43752 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.60 | 0.92 | 21 | empty |
| 2 | 110 | 0.56 | 0.84 | 24 | empty |
| 3 | 98 | 0.44 | 0.78 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 804 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 617 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 108 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4J2C · GARP-SNARE Interaction · the same entry in another collection · chain A against A, TM-score 1.00
- O43752 · AlphaFold monomer V2.0 prediction for syntaxin-6 (O43752) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q9UID3 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 51… · a predicted model of the same protein · chain B against A, TM-score 0.71
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 O43752
- Every structure of UniProt Q9UID3
- Elsewhere: RCSB PDB 4J2C · PDBe 4J2C · UniProt O43752 · UniProt Q9UID3
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