MolNFT v1 · #156728 · protein
The 20S supercomplex engaging the snap-25 N-terminus (class 1)
6MDM · Vesicle-fusing ATPase: “The 20S supercomplex engaging the snap-25 N-terminus (class 1)”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.87). MolNFT v1 #156728 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MDM
- Type
- protein
- Length
- 4,651 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 0.87
Structure
electron microscopy · 10 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 699 | 35% helix, 20% strand | P18708 |
| B | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 704 | 36% helix, 20% strand | P18708 |
| C | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 709 | 37% helix, 18% strand | P18708 |
| D | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 713 | 35% helix, 19% strand | P18708 |
| E | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 514 | 45% helix, 8% strand | P18708 |
| F | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 466 | 42% helix, 10% strand | P18708 |
| H | Synaptosomal-associated protein 25 | protein | 147 | 80% helix, 1% strand | P60881 |
| I | Syntaxin-1A | protein | 66 | 88% helix, 0% strand | P32851 |
| J | Vesicle-associated membrane protein 2 | protein | 61 | 92% helix, 0% strand | P63045 |
| K, L | Alpha-soluble nsf attachment protein | protein | 286 | 69% 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 | 695 | 0.87 | 0.90 | 94 | ATP |
| 2 | 1111 | 0.86 | 0.87 | 112 | ATP |
| 3 | 602 | 0.85 | 0.90 | 64 | ATP |
| 4 | 710 | 0.85 | 0.88 | 72 | ATP |
| 5 | 918 | 0.84 | 0.86 | 81 | empty |
Interfaces
29 interfaces between chains.
- C–D · 4061 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3926 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 3894 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 3883 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2323 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6MDM · The 20S supercomplex engaging the SNAP-25 N-terminus (class 1) · 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 0.92
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 6MDM · PDBe 6MDM · UniProt P18708 · UniProt P60881 · UniProt P32851 · UniProt P63045 · UniProt P54921
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