Research workbench
Crystal structure of human vat-1
Analyse Crystal structure of human vat-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K9Y
- Type
- protein
- Length
- 1,328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptic vesicle membrane protein vat-1 homolog
- EC
- 1.-.-.-
- UniProt
- Q99536
- Ligands
- NO3
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synaptic vesicle membrane protein vat-1 homolog (EC 1.-.-.-) | protein | 342 | 34% helix, 27% strand | Q99536 |
| B | Synaptic vesicle membrane protein vat-1 homolog (EC 1.-.-.-) | protein | 328 | 34% helix, 29% strand | Q99536 |
| C | Synaptic vesicle membrane protein vat-1 homolog (EC 1.-.-.-) | protein | 325 | 34% helix, 28% strand | Q99536 |
| D | Synaptic vesicle membrane protein vat-1 homolog (EC 1.-.-.-) | protein | 333 | 34% helix, 27% strand | Q99536 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.84 | 0.94 | 62 | NO3 |
| 2 | 399 | 0.82 | 0.90 | 63 | NO3 |
| 3 | 220 | 0.82 | 0.95 | 39 | NO3 |
| 4 | 302 | 0.81 | 0.92 | 49 | NO3 |
| 5 | 545 | 0.67 | 0.77 | 55 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1615 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1601 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 474 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 308 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 125 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q99536
- Elsewhere: RCSB PDB 6K9Y · PDBe 6K9Y · UniProt Q99536
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