Research workbench
The 20S supercomplex engaging the snap-25 N-terminus (class 2)
Analyse The 20S supercomplex engaging the snap-25 N-terminus (class 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MDN
- Type
- protein
- Length
- 4,632 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-fusing ATPase; Synaptosomal-associated protein 25; Syntaxin-1A…
- EC
- 3.6.4.6
- UniProt
- P18708, P60881, P32851, P63045, P54921
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 10 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 511 | 44% helix, 11% strand | P18708 |
| B | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 707 | 36% helix, 19% strand | P18708 |
| C | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 709 | 37% helix, 19% strand | P18708 |
| D | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 713 | 37% helix, 19% strand | P18708 |
| E | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 697 | 37% helix, 17% strand | P18708 |
| F | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 449 | 43% helix, 10% strand | P18708 |
| H | Synaptosomal-associated protein 25 | protein | 147 | 81% helix, 1% strand | P60881 |
| I | Syntaxin-1A | protein | 66 | 91% helix, 0% strand | P32851 |
| J | Vesicle-associated membrane protein 2 | protein | 61 | 89% helix, 0% strand | P63045 |
| K, L | Alpha-soluble nsf attachment protein | protein | 286 | 71% helix, 0% strand | P54921 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 9 copies · chains A, F, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.86 | 0.87 | 130 | ATP |
| 2 | 718 | 0.86 | 0.90 | 87 | ATP |
| 3 | 984 | 0.86 | 0.87 | 86 | ATP |
| 4 | 705 | 0.86 | 0.89 | 74 | ATP |
| 5 | 1066 | 0.85 | 0.86 | 111 | empty |
Interfaces
28 interfaces between chains.
- C–D · 3849 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3772 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 3688 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 3642 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2402 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6MDN · The 20S supercomplex engaging the SNAP-25 N-terminus (class 2) · the same entry in another collection · chain L against L, TM-score 1.00
- P54921 · AlphaFold monomer V2.0 prediction for alpha-soluble nsf attachment protein (P54921) · a predicted model of the same protein · chain K against A, TM-score 0.91
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 P18708
- Every structure of UniProt P60881
- Every structure of UniProt P32851
- Every structure of UniProt P63045
- Every structure of UniProt P54921
- Elsewhere: RCSB PDB 6MDN · PDBe 6MDN · UniProt P18708 · UniProt P60881 · UniProt P32851 · UniProt P63045 · UniProt P54921
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