MolNFT v1 · #12497 · protein
Three-dimensional structure of the COMPLEXIN/SNARE complex
1KIL · Synaptobrevin snare motif: “Three-dimensional structure of the COMPLEXIN/SNARE complex”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.60). MolNFT v1 #12497 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1KIL
- Type
- protein
- Length
- 303 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptobrevin snare motif; Syntaxin snare motif short; Snap-25 N-terminal snare motif…
- UniProt
- P63045, P32851, P60880, P63041
- Ligands
- MG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synaptobrevin snare motif | protein | 65 | 91% helix, 0% strand | P63045 |
| B | Syntaxin snare motif short | protein | 59 | 93% helix, 0% strand | P32851 |
| C | Snap-25 N-terminal snare motif | protein | 72 | 96% helix, 0% strand | P60880 |
| D | Snap-25 C-terminal snare motif | protein | 66 | 92% helix, 0% strand | P60880 |
| E | Complexin I snare-complex binding region | protein | 41 | 88% helix, 0% strand | P63041 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.60 | 0.86 | 15 | empty |
| 2 | 156 | 0.48 | 0.77 | 22 | empty |
| 3 | 153 | 0.43 | 0.75 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1527 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1522 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1488 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1451 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 660 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1KIL · Three-dimensional structure of the complexin/SNARE complex · the same entry in another collection · chain E against E, TM-score 1.00
- P60880 · AlphaFold monomer V2.0 prediction for synaptosomal-associated protein 25 (P60880) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P63041 · AlphaFold monomer V2.0 prediction for complexin-1 (P63041) · a predicted model of the same protein · chain E against A, TM-score 0.91
- 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
- P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B 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 P60880
- Every structure of UniProt P63041
- Elsewhere: RCSB PDB 1KIL · PDBe 1KIL · UniProt P63045 · UniProt P32851 · UniProt P60880 · UniProt P63041
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