MolNFT v1 · #166921 · protein
Full extracellular region of zebrafish GPR126/ADGRG6
6V55 · Adhesion G-protein coupled receptor G6: “Full extracellular region of zebrafish GPR126/ADGRG6”. X-ray diffraction, 2 ligands (NAG, CA), 4 pockets (best druggability 0.66). MolNFT v1 #166921 on GenesisL1: 3D structure, binding sites…
- PDB
- 6V55
- Type
- protein
- Length
- 753 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adhesion G-protein coupled receptor G6
- UniProt
- C6KFA3
- Ligands
- NAG, CA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adhesion G-protein coupled receptor G6 | protein | 746 | 16% helix, 36% strand | C6KFA3 |
| Q | Adhesion G-protein coupled receptor G6 | protein | 7 | 0% helix, 71% strand | C6KFA3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.66 | 0.84 | 34 | empty |
| 2 | 197 | 0.50 | 0.77 | 27 | empty |
| 3 | 59 | 0.32 | 0.77 | 15 | empty |
| 4 | 53 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–Q · 840 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 6V55 · Full extracellular region of zebrafish Gpr126/Adgrg6 · the same entry in another collection · chain A against A, TM-score 1.00
- C6KFA3 · AlphaFold monomer V2.0 prediction for adhesion G-protein coupled receptor G6 (C6KFA3) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 C6KFA3
- Elsewhere: RCSB PDB 6V55 · PDBe 6V55 · UniProt C6KFA3
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