MolNFT v1 · #158033 · protein
Stabilized beta-arrestin 1-V2T subcomplex of a GPCR-G protein-beta- arrestin mega-complex
6NI2 · Nanobody 32: “Stabilized beta-arrestin 1-V2T subcomplex of a GPCR-G protein-beta- arrestin mega-complex”. Electron microscopy, 10 pockets (best druggability 0.80). MolNFT v1 #158033 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NI2
- Type
- protein
- Length
- 704 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody 32; Beta-arrestin-1; FAB30 heavy chain; FAB30 light chain; Vasopressin V2…
- UniProt
- P17870, P30518
- Pockets
- 10 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 2% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody 32 | protein | 113 | 0% helix, 22% strand | — |
| B | Beta-arrestin-1 | protein | 353 | 4% helix, 46% strand | P17870 |
| H | FAB30 heavy chain | protein | 117 | 3% helix, 55% strand | — |
| L | FAB30 light chain | protein | 107 | 0% helix, 48% strand | — |
| V | Vasopressin V2 receptor | protein | 14 | 0% helix, 29% strand | P30518 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.80 | 0.82 | 107 | empty |
| 2 | 176 | 0.63 | 0.85 | 34 | empty |
| 3 | 102 | 0.58 | 0.86 | 24 | empty |
| 4 | 188 | 0.48 | 0.76 | 34 | empty |
| 5 | 134 | 0.47 | 0.77 | 17 | empty |
Interfaces
8 interfaces between chains.
- B–V · 887 Ų buried · 27 hydrogen bonds · protein-protein
- H–L · 786 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 607 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 599 Ų buried · 4 hydrogen bonds · protein-protein
- A–V · 269 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 disulfide (phosphorylation, disulfide).
Compared structures
- 6NI2 · Stabilized beta-arrestin 1-V2T subcomplex of a GPCR-G protein-beta-arrestin mega-complex · the same entry in another collection · chain B against B, TM-score 1.00
- P17870 · AlphaFold monomer V2.0 prediction for beta-arrestin-1 (P17870) · a predicted model of the same protein · chain B against A, TM-score 0.83
- P30518 · AlphaFold monomer V2.0 prediction for vasopressin V2 receptor (P30518) · a predicted model of the same protein · chain V against A, TM-score 0.22
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 P17870
- Every structure of UniProt P30518
- Elsewhere: RCSB PDB 6NI2 · PDBe 6NI2 · UniProt P17870 · UniProt P30518
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