MolNFT v1 · #68125 · protein
Structure of ADP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy
3J95 · Vesicle-fusing ATPase: “Structure of ADP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #68125 on…
- PDB
- 3J95
- Type
- protein
- Length
- 2,883 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
- ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 483 | 52% helix, 12% strand | P18708 |
| B | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 481 | 49% helix, 12% strand | P18708 |
| C | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 485 | 51% helix, 12% strand | P18708 |
| D | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 479 | 50% helix, 13% strand | P18708 |
| E | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 482 | 51% helix, 12% strand | P18708 |
| F | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 473 | 50% helix, 13% strand | P18708 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains 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 | 1063 | 0.86 | 0.87 | 123 | ADP |
| 2 | 628 | 0.85 | 0.89 | 66 | ADP |
| 3 | 1190 | 0.84 | 0.85 | 105 | ADP |
| 4 | 479 | 0.83 | 0.90 | 64 | empty |
| 5 | 1135 | 0.82 | 0.83 | 127 | ADP |
Interfaces
6 interfaces between chains.
- E–F · 2469 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2235 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 2133 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1989 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1947 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 covalent (covalent ligand).
Compared structures
- 3J95 · Structure of ADP-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 E against A, TM-score 0.93
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 3J95 · PDBe 3J95 · UniProt P18708
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