MolNFT v1 · #67609 · protein
Helical extension of the neuronal snare complex into the membrane, spacegroup I 21 21 21
3IPD · Vesicle-associated membrane protein 2: “Helical extension of the neuronal snare complex into the membrane, spacegroup I 21 21 21”. X-ray diffraction, 7 pockets (best druggability 0.72). MolNFT v1 #67609 on GenesisL1: 3D structure…
- PDB
- 3IPD
- Type
- protein
- Length
- 654 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-associated membrane protein 2; Syntaxin-1A; Synaptosomal-associated protein 25
- UniProt
- P63045, P32851, P60881
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Vesicle-associated membrane protein 2 | protein | 91 | 81% helix, 0% strand | P63045 |
| B, F | Syntaxin-1A | protein | 98 | 83% helix, 0% strand | P32851 |
| C, G | Synaptosomal-associated protein 25 | protein | 75 | 76% helix, 0% strand | P60881 |
| D, H | Synaptosomal-associated protein 25 | protein | 63 | 79% helix, 0% strand | P60881 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.72 | 0.86 | 38 | empty |
| 2 | 51 | 0.65 | 0.95 | 19 | empty |
| 3 | 327 | 0.63 | 0.80 | 23 | empty |
| 4 | 150 | 0.60 | 0.84 | 24 | empty |
| 5 | 155 | 0.49 | 0.77 | 26 | empty |
Interfaces
18 interfaces between chains.
- E–F · 2255 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2213 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1628 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1506 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 1383 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3IPD · Helical extension of the neuronal SNARE complex into the membrane, spacegroup I 21 21 21 · the same entry in another collection · chain H against H, TM-score 1.00
- P60881 · AlphaFold monomer V2.0 prediction for synaptosomal-associated protein 25 (P60881) · a predicted model of the same protein · chain C against A, TM-score 0.94
- P63045 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 2 (P63045) · a predicted model of the same protein · chain A against A, TM-score 0.78
- P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B against A, TM-score 0.65
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 P63045
- Every structure of UniProt P32851
- Every structure of UniProt P60881
- Elsewhere: RCSB PDB 3IPD · PDBe 3IPD · UniProt P63045 · UniProt P32851 · UniProt P60881
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