MolNFT v1 · #189141 · protein
Crystal structure of vpsr display novel dimeric architecture and C-di- gmp binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.
7V3W: “Crystal structure of vpsr display novel dimeric architecture and C-di- gmp binding: mechanistic implications…”. X-ray diffraction, 1 ligand (ATP), 17 pockets (best druggability 0.85). MolNFT v1 #189141 on GenesisL1: 3D structure…
- PDB
- 7V3W
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vpsr
- UniProt
- Q9AQ41
- Ligands
- ATP
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vpsr | protein | 374 | 41% helix, 13% strand | Q9AQ41 |
| D | Vpsr | protein | 376 | 41% helix, 13% strand | Q9AQ41 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.85 | 0.87 | 89 | empty |
| 2 | 97 | 0.76 | 0.96 | 26 | empty |
| 3 | 105 | 0.75 | 0.95 | 19 | empty |
| 4 | 325 | 0.70 | 0.83 | 43 | empty |
| 5 | 117 | 0.70 | 0.91 | 24 | empty |
Interfaces
1 interface between chains.
- A–D · 3244 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 7V3W · Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9AQ41
- Elsewhere: RCSB PDB 7V3W · PDBe 7V3W · UniProt Q9AQ41
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