MolNFT v1 · #155763 · protein
Crystal structure of the complex between vesicle amine transport-1 and NADP
6LHR · Synaptic vesicle membrane protein vat-1 homolog: “Crystal structure of the complex between vesicle amine transport-1 and NADP”. X-ray diffraction, 1 ligand (NAP), 10 pockets (best druggability 0.86). MolNFT v1 #155763 on GenesisL1…
- PDB
- 6LHR
- Type
- protein
- Length
- 1,362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptic vesicle membrane protein vat-1 homolog
- UniProt
- Q99536
- Ligands
- NAP
- Pockets
- 10 · best druggability 0.86
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 | protein | 343 | 35% helix, 28% strand | Q99536 |
| B | Synaptic vesicle membrane protein vat-1 homolog | protein | 338 | 33% helix, 28% strand | Q99536 |
| C | Synaptic vesicle membrane protein vat-1 homolog | protein | 344 | 35% helix, 28% strand | Q99536 |
| D | Synaptic vesicle membrane protein vat-1 homolog | protein | 337 | 34% helix, 29% strand | Q99536 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.86 | 0.90 | 75 | NAP |
| 2 | 539 | 0.85 | 0.91 | 59 | NAP |
| 3 | 837 | 0.83 | 0.85 | 85 | NAP |
| 4 | 891 | 0.82 | 0.84 | 94 | NAP |
| 5 | 103 | 0.64 | 0.89 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1559 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1527 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 829 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 790 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 201 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LHR · Crystal structure of the complex between Vesicle Amine Transport-1 and NADP · the same entry in another collection · chain D against D, TM-score 1.00
- Q99536 · AlphaFold monomer V2.0 prediction for synaptic vesicle membrane protein vat-1 homolog… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 6LHR · PDBe 6LHR · UniProt Q99536
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