Research workbench
Crystal structure of human synaptic vesicle membrane protein vat-1 homolog-like protein
Analyse Crystal structure of human synaptic vesicle membrane protein vat-1 homolog-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A27
- Type
- protein
- Length
- 623 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptic vesicle membrane protein vat-1 homolog-like
- EC
- 1.-.-.-
- UniProt
- Q9HCJ6
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synaptic vesicle membrane protein vat-1 homolog-like (EC 1.-.-.-) | protein | 314 | 32% helix, 30% strand | Q9HCJ6 |
| B | Synaptic vesicle membrane protein vat-1 homolog-like (EC 1.-.-.-) | protein | 309 | 33% helix, 30% strand | Q9HCJ6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.79 | 0.85 | 61 | empty |
| 2 | 441 | 0.78 | 0.87 | 52 | EDO |
| 3 | 234 | 0.63 | 0.82 | 37 | EDO |
| 4 | 68 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1416 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4A27 · Crystal structure of human synaptic vesicle membrane protein VAT-1 homolog-like protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HCJ6 · AlphaFold monomer V2.0 prediction for synaptic vesicle membrane protein vat-1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9HCJ6
- Elsewhere: RCSB PDB 4A27 · PDBe 4A27 · UniProt Q9HCJ6
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