Research workbench
Structure of the MG2+-bound synaptotagmin-1 snare complex (short unit cell form)
Analyse Structure of the MG2+-bound synaptotagmin-1 snare complex (short unit cell form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CCI
- Type
- protein
- Length
- 814 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-associated membrane protein 2; Syntaxin-1A; Synaptosomal-associated protein 25…
- UniProt
- P63045, P32851, P60881, P21707
- Ligands
- MG
- Pockets
- 6 · best druggability 0.48
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-associated membrane protein 2 | protein | 62 | 97% helix, 0% strand | P63045 |
| B | Syntaxin-1A | protein | 67 | 96% helix, 0% strand | P32851 |
| C | Synaptosomal-associated protein 25 | protein | 73 | 97% helix, 0% strand | P60881 |
| D | Synaptosomal-associated protein 25 | protein | 64 | 95% helix, 0% strand | P60881 |
| E | Synaptotagmin-1 | protein | 280 | 9% helix, 46% strand | P21707 |
| F | Synaptotagmin-1 | protein | 268 | 10% helix, 45% strand | P21707 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.48 | 0.78 | 21 | empty |
| 2 | 174 | 0.48 | 0.77 | 25 | empty |
| 3 | 124 | 0.39 | 0.75 | 24 | empty |
| 4 | 113 | 0.39 | 0.75 | 18 | empty |
| 5 | 55 | 0.38 | 0.80 | 11 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1630 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1591 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1530 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1454 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 519 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5CCI · Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form) · the same entry in another collection · chain F against F, TM-score 1.00
- P60881 · AlphaFold monomer V2.0 prediction for synaptosomal-associated protein 25 (P60881) · a predicted model of the same protein · chain D against A, TM-score 0.97
- 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 0.83
- P21707 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21707) · a predicted model of the same protein · chain E against A, TM-score 0.82
- P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 P21707
- Elsewhere: RCSB PDB 5CCI · PDBe 5CCI · UniProt P63045 · UniProt P32851 · UniProt P60881 · UniProt P21707
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