MolNFT v1 · #28955 · protein
Maltose-binding protein fusion to a C-terminal fragment of the V1A vasopressin receptor
1YTV · Maltose-binding periplasmic protein: “Maltose-binding protein fusion to a C-terminal fragment of the V1A vasopressin receptor”. X-ray diffraction, 1 ligand (GLC), 8 pockets (best druggability 0.72). MolNFT v1 #28955 on GenesisL1: 3D…
- PDB
- 1YTV
- Type
- protein
- Length
- 743 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein; Vasopressin V1A receptor
- UniProt
- P02928, P37288
- Ligands
- GLC
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltose-binding periplasmic protein | protein | 366 | 46% helix, 21% strand | P02928 |
| M | Vasopressin V1A receptor | protein | 6 | 0% helix, 0% strand | P37288 |
| N | Vasopressin V1A receptor | protein | 5 | 0% helix, 0% strand | P37288 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.72 | 0.85 | 29 | GLC |
| 2 | 305 | 0.70 | 0.84 | 34 | GLC |
| 3 | 480 | 0.68 | 0.79 | 44 | empty |
| 4 | 71 | 0.38 | 0.77 | 14 | empty |
| 5 | 65 | 0.37 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 596 Ų buried · 15 hydrogen bonds · protein-protein
- A–M · 369 Ų buried · 16 hydrogen bonds · protein-protein
- B–N · 319 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1YTV · Maltose-binding protein fusion to a C-terminal fragment of the V1a vasopressin receptor · the same entry in another collection · chain B against B, TM-score 1.00
- P37288 · AlphaFold monomer V2.0 prediction for vasopressin V1A receptor (P37288) · a predicted model of the same protein · chain N against A, TM-score 0.59
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 P02928
- Every structure of UniProt P37288
- Elsewhere: RCSB PDB 1YTV · PDBe 1YTV · UniProt P02928 · UniProt P37288
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