MolNFT v1 · #124577 · protein
Structure of the CA2+-bound synaptotagmin-1 snare complex (long unit cell form) - from synchrotron diffraction
5KJ8 · Vesicle-associated membrane protein 3: “Structure of the CA2+-bound synaptotagmin-1 snare complex (long unit cell form) - from synchrotron diffraction”. X-ray diffraction, 1 ligand (CA), 11 pockets (best druggability 0.43). MolNFT…
- PDB
- 5KJ8
- Type
- protein
- Length
- 1,361 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-associated membrane protein 3; Syntaxin-1A; Synaptosomal-associated protein 25…
- UniProt
- P63025, P32851, P60881, P21707
- Ligands
- CA
- Pockets
- 11 · best druggability 0.43
Structure
x-ray diffraction · 9 distinct chains · 49% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Vesicle-associated membrane protein 3 | protein | 63 | 97% helix, 0% strand | P63025 |
| B | Syntaxin-1A | protein | 66 | 95% helix, 0% strand | P32851 |
| C | Synaptosomal-associated protein 25 | protein | 74 | 96% helix, 0% strand | P60881 |
| D | Synaptosomal-associated protein 25 | protein | 63 | 94% helix, 0% strand | P60881 |
| E, K | Synaptotagmin-1 | protein | 278 | 10% helix, 46% strand | P21707 |
| F | Synaptotagmin-1 | protein | 274 | 10% helix, 46% strand | P21707 |
| H | Syntaxin-1A | protein | 65 | 95% helix, 0% strand | P32851 |
| I | Synaptosomal-associated protein 25 | protein | 74 | 96% helix, 0% strand | P60881 |
| J | Synaptosomal-associated protein 25 | protein | 63 | 92% helix, 0% strand | P60881 |
Ligands and binding sites
- CA · Calcium ion · metal · 14 copies · chains C, D, E, F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.43 | 0.75 | 27 | empty |
| 2 | 136 | 0.43 | 0.76 | 22 | empty |
| 3 | 96 | 0.41 | 0.78 | 20 | CA |
| 4 | 151 | 0.41 | 0.74 | 25 | empty |
| 5 | 67 | 0.38 | 0.79 | 17 | empty |
Interfaces
24 interfaces between chains.
- A–B · 1638 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 1554 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1552 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1485 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1482 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5KJ8 · Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from… · the same entry in another collection · chain K against K, 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 0.96
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 P63025
- Every structure of UniProt P32851
- Every structure of UniProt P60881
- Every structure of UniProt P21707
- Elsewhere: RCSB PDB 5KJ8 · PDBe 5KJ8 · UniProt P63025 · UniProt P32851 · UniProt P60881 · UniProt P21707
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