Research workbench
Cryo-EM structure of a synaptobrevin-MUNC18-1-syntaxin-1 complex class 2
Analyse Cryo-EM structure of a synaptobrevin-MUNC18-1-syntaxin-1 complex class 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UDB
- Type
- protein
- Length
- 807 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntaxin-binding protein 1; Syntaxin-1A; Synaptobrevin-2
- UniProt
- P61765, P32851, P63045
- Pockets
- 12 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syntaxin-binding protein 1 | protein | 551 | 47% helix, 14% strand | P61765 |
| B | Syntaxin-1A | protein | 208 | 78% helix, 0% strand | P32851 |
| C | Synaptobrevin-2 | protein | 48 | 90% helix, 2% strand | P63045 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.79 | 0.81 | 103 | empty |
| 2 | 916 | 0.75 | 0.78 | 77 | empty |
| 3 | 281 | 0.67 | 0.83 | 36 | empty |
| 4 | 157 | 0.57 | 0.82 | 34 | empty |
| 5 | 162 | 0.45 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2646 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1341 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7UDB · Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2 · the same entry in another collection · chain A against A, TM-score 1.00
- P61765 · AlphaFold monomer V2.0 prediction for syntaxin-binding protein 1 (P61765) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P63045 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 2 (P63045) · a predicted model of the same protein · chain C against A, TM-score 0.72
- P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B against A, TM-score 0.64
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 P61765
- Every structure of UniProt P32851
- Every structure of UniProt P63045
- Elsewhere: RCSB PDB 7UDB · PDBe 7UDB · UniProt P61765 · UniProt P32851 · UniProt P63045
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