MolNFT v1 · #45402 · protein
Dynamic binding mode of a synaptotagmin-1-snare complex in solution
2N1T · Vesicle-associated membrane protein 2: “Dynamic binding mode of a synaptotagmin-1-snare complex in solution”. Solution nmr, 6 pockets (best druggability 0.67). MolNFT v1 #45402 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2N1T
- Type
- protein
- Length
- 448 residues
- Chains
- 5
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-associated membrane protein 2; Syntaxin-1A; Synaptosomal-associated protein 25…
- UniProt
- P63045, P32851, P60880, P21579
- Pockets
- 6 · best druggability 0.67
Structure
solution nmr · 5 distinct chains · 64% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-associated membrane protein 2 | protein | 69 | 90% helix, 0% strand | P63045 |
| B | Syntaxin-1A | protein | 72 | 92% helix, 0% strand | P32851 |
| C | Synaptosomal-associated protein 25 | protein | 77 | 91% helix, 0% strand | P60880 |
| D | Synaptosomal-associated protein 25 | protein | 74 | 81% helix, 0% strand | P60880 |
| E | Synaptotagmin-1 | protein | 156 | 17% helix, 41% strand | P21579 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.67 | 0.84 | 28 | empty |
| 2 | 225 | 0.51 | 0.76 | 30 | empty |
| 3 | 139 | 0.49 | 0.78 | 24 | empty |
| 4 | 86 | 0.43 | 0.79 | 20 | empty |
| 5 | 52 | 0.30 | 0.76 | 11 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1683 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1654 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1627 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1480 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 534 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2N1T · Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution · the same entry in another collection · chain E against E, TM-score 1.00
- P21579 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21579) · a predicted model of the same protein · chain E against A, TM-score 0.91
- P60880 · AlphaFold monomer V2.0 prediction for synaptosomal-associated protein 25 (P60880) · a predicted model of the same protein · chain C against A, TM-score 0.84
- P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B against A, TM-score 0.76
- 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 0.74
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 P60880
- Every structure of UniProt P21579
- Elsewhere: RCSB PDB 2N1T · PDBe 2N1T · UniProt P63045 · UniProt P32851 · UniProt P60880 · UniProt P21579
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