MolNFT v1 · #156731 · 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 2)
6MDP · 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 #156731 on…
- PDB
- 6MDP
- Type
- protein
- Length
- 2,832 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 · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 511 | 45% helix, 10% strand | P18708 |
| B | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 516 | 44% helix, 10% strand | P18708 |
| C | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 527 | 42% helix, 10% strand | P18708 |
| D | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 526 | 43% helix, 8% strand | P18708 |
| E | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 492 | 43% helix, 10% strand | P18708 |
| F | Vesicle-fusing ATPase (EC 3.6.4.6) | protein | 243 | 49% helix, 12% strand | P18708 |
| H | Synaptosomal-associated protein 25 | protein | 17 | 0% helix, 0% strand | P60881 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 9 copies · chains A, B, C, D, E, F
- 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 | 723 | 0.86 | 0.89 | 73 | ATP |
| 2 | 822 | 0.86 | 0.88 | 93 | ATP |
| 3 | 645 | 0.86 | 0.90 | 64 | ATP |
| 4 | 549 | 0.85 | 0.91 | 58 | ATP |
| 5 | 254 | 0.84 | 0.95 | 44 | empty |
Interfaces
13 interfaces between chains.
- B–C · 4050 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3876 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3720 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 3617 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 1559 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6MDP · The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S… · the same entry in another collection · chain D against D, 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 6MDP · PDBe 6MDP · UniProt P18708 · UniProt P60881
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