MolNFT v1 · #156730 · protein
The D1 and D2 domain rings of nsf engaging the snap-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 1)
6MDO · Vesicle-fusing ATPase: “The D1 and D2 domain rings of nsf engaging the snap-25 N-terminus within the 20S supercomplex (focused…”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.86). MolNFT v1 #156730 on…
- PDB
- 6MDO
- Type
- protein
- Length
- 2,843 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-fusing ATPase; Synaptosomal-associated protein 25
- EC
- 3.6.4.6
- UniProt
- P18708, P60881
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 511 | 43% helix, 11% strand | P18708 |
| B | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 519 | 45% helix, 12% strand | P18708 |
| C | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 521 | 45% helix, 10% strand | P18708 |
| D | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 525 | 47% helix, 10% strand | P18708 |
| E | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 509 | 44% helix, 9% strand | P18708 |
| F | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 241 | 46% helix, 12% strand | P18708 |
| H | Synaptosomal-associated protein 25 | protein | 17 | 0% helix, 12% strand | P60881 |
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 | 698 | 0.86 | 0.90 | 63 | ATP |
| 2 | 761 | 0.86 | 0.89 | 98 | ATP |
| 3 | 926 | 0.86 | 0.87 | 99 | ATP |
| 4 | 659 | 0.85 | 0.89 | 73 | ATP |
| 5 | 1110 | 0.85 | 0.86 | 120 | ATP |
Interfaces
15 interfaces between chains.
- D–E · 3858 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 3816 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 3752 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3585 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1475 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6MDO · The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S… · the same entry in another collection · chain A against A, 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 P60881
- Elsewhere: RCSB PDB 6MDO · PDBe 6MDO · UniProt P18708 · UniProt P60881
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