Research workbench
Structure of mouse BAI1 (ADGRB1) in complex with mouse nogo receptor (RTN4R)
Analyse Structure of mouse BAI1 (ADGRB1) in complex with mouse nogo receptor (RTN4R) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R86
- Type
- protein
- Length
- 653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulon-4 receptor; Vasculostatin-120
- UniProt
- Q99PI8, Q3UHD1
- Ligands
- PAB, NAG, MAN, FUC, BGC, CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulon-4 receptor | protein | 284 | 8% helix, 17% strand | Q99PI8 |
| B | Reticulon-4 receptor | protein | 285 | 8% helix, 17% strand | Q99PI8 |
| C | Vasculostatin-120 | protein | 44 | 0% helix, 32% strand | Q3UHD1 |
| D | Vasculostatin-120 | protein | 40 | 0% helix, 35% strand | Q3UHD1 |
Ligands and binding sites
- PAB · 4-aminobenzoic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, C, B, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C, B, D
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, B
- PG4 · Tetraethylene glycol · additive · chains A
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.70 | 0.77 | 67 | EDO, MAN |
| 2 | 234 | 0.56 | 0.78 | 39 | PAB |
| 3 | 141 | 0.37 | 0.73 | 17 | MAN |
Interfaces
5 interfaces between chains.
- A–C · 559 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 444 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 256 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 255 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 10 glycan (disulfide, C-mannosylation, N-glycosylation, O-glycosylation).
Compared structures
- 7R86 · Structure of mouse BAI1 (ADGRB1) in complex with mouse Nogo receptor (RTN4R) · the same entry in another collection · chain D against D, TM-score 1.00
- Q99PI8 · AlphaFold monomer V2.0 prediction for reticulon-4 receptor (Q99PI8) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q3UHD1 · AlphaFold monomer V2.0 prediction for adhesion G protein-coupled receptor B1 (Q3UHD1) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 Q99PI8
- Every structure of UniProt Q3UHD1
- Elsewhere: RCSB PDB 7R86 · PDBe 7R86 · UniProt Q99PI8 · UniProt Q3UHD1
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