Research workbench
Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy
Analyse Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J94
- Type
- protein
- Length
- 2,895 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-fusing ATPase
- EC
- 3.6.4.6
- UniProt
- P18708
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 490 | 51% helix, 11% strand | P18708 |
| B | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 484 | 50% helix, 13% strand | P18708 |
| C | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 488 | 51% helix, 13% strand | P18708 |
| D | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 485 | 50% helix, 12% strand | P18708 |
| E | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 482 | 50% helix, 12% strand | P18708 |
| F | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 466 | 50% helix, 14% strand | P18708 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 11 copies · chains A, F, B, C, 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 | 927 | 0.85 | 0.86 | 99 | ATP |
| 2 | 686 | 0.85 | 0.89 | 67 | ATP |
| 3 | 621 | 0.84 | 0.89 | 74 | ATP |
| 4 | 1153 | 0.83 | 0.84 | 155 | ATP |
| 5 | 960 | 0.83 | 0.84 | 111 | ATP |
Interfaces
6 interfaces between chains.
- C–D · 2789 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2747 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2556 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2514 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 2089 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 covalent (covalent ligand).
Compared structures
- 3J94 · Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single particle… · the same entry in another collection · chain F against F, TM-score 1.00
- P18708 · AlphaFold monomer V2.0 prediction for vesicle-fusing ATPase (P18708) · a predicted model of the same protein · chain C against A, TM-score 0.97
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
- Elsewhere: RCSB PDB 3J94 · PDBe 3J94 · UniProt P18708
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.