Research workbench
Structure of 20S supercomplex determined by single particle cryoelectron microscopy (state II)
Analyse Structure of 20S supercomplex determined by single particle cryoelectron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J97
- Type
- protein
- Length
- 5,425 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-fusing ATPase; Alpha-soluble nsf attachment protein; Vesicle-associated membrane…
- EC
- 3.6.4.6
- UniProt
- P18708, P54921, P63045, P32851
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 10 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 678 | 40% helix, 21% strand | P18708 |
| B | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 672 | 38% helix, 21% strand | P18708 |
| C | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 676 | 39% helix, 22% strand | P18708 |
| D | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 673 | 38% helix, 21% strand | P18708 |
| E | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 670 | 39% helix, 22% strand | P18708 |
| F | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 654 | 38% helix, 22% strand | P18708 |
| H, I, J, G | Alpha-soluble nsf attachment protein | protein | 286 | 72% helix, 0% strand | P54921 |
| K | Vesicle-associated membrane protein 2 | protein | 61 | 93% helix, 0% strand | P63045 |
| L | Syntaxin-1A | protein | 66 | 92% helix, 0% strand | P32851 |
| M | Synaptosomal-associated protein 25 | protein | 131 | 92% helix, 0% strand | — |
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 | 987 | 0.88 | 0.89 | 121 | empty |
| 2 | 909 | 0.84 | 0.86 | 114 | empty |
| 3 | 782 | 0.83 | 0.86 | 70 | empty |
| 4 | 1139 | 0.83 | 0.84 | 122 | empty |
| 5 | 973 | 0.83 | 0.84 | 107 | empty |
Interfaces
33 interfaces between chains.
- C–D · 2859 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2678 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2556 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2455 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2197 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3J97 · Structure of 20S supercomplex determined by single particle cryoelectron microscopy… · the same entry in another collection · chain M against M, TM-score 1.00
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 P54921
- Every structure of UniProt P63045
- Every structure of UniProt P32851
- Elsewhere: RCSB PDB 3J97 · PDBe 3J97 · UniProt P18708 · UniProt P54921 · UniProt P63045 · UniProt P32851
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