Research workbench
Alpha-snap-snare subcomplex in the whole 20S complex
Analyse Alpha-snap-snare subcomplex in the whole 20S complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IP1
- Type
- protein
- Length
- 1,420 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-associated membrane protein 2; Syntaxin-1A; Synaptosomal-associated protein 25…
- UniProt
- P63045, P32851, P60881, A5D7S0
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-associated membrane protein 2 | protein | 63 | 86% helix, 0% strand | P63045 |
| B | Syntaxin-1A | protein | 62 | 90% helix, 0% strand | P32851 |
| C | Synaptosomal-associated protein 25 | protein | 65 | 91% helix, 0% strand | P60881 |
| D | Synaptosomal-associated protein 25 | protein | 62 | 94% helix, 0% strand | P60881 |
| E, F, G, H | Alpha-soluble nsf attachment protein | protein | 292 | 73% helix, 0% strand | A5D7S0 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.87 | 0.90 | 104 | empty |
| 2 | 560 | 0.84 | 0.90 | 86 | empty |
| 3 | 417 | 0.81 | 0.90 | 52 | empty |
| 4 | 279 | 0.78 | 0.90 | 41 | empty |
| 5 | 292 | 0.74 | 0.87 | 39 | empty |
Interfaces
26 interfaces between chains.
- B–C · 1488 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1402 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1400 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1325 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 675 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6IP1 · alpha-SNAP-SNARE subcomplex in the whole 20S complex · the same entry in another collection · chain H against H, TM-score 1.00
- P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B against A, TM-score 0.82
- P63045 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 2 (P63045) · a predicted model of the same protein · chain A against A, TM-score 0.79
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 P63045
- Every structure of UniProt P32851
- Every structure of UniProt P60881
- Every structure of UniProt A5D7S0
- Elsewhere: RCSB PDB 6IP1 · PDBe 6IP1 · UniProt P63045 · UniProt P32851 · UniProt P60881 · UniProt A5D7S0
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