MolNFT v1 · #128772 · protein
Deglycosylated nogo receptor with native disulfide structure
5O0Q · Reticulon-4 receptor: “Deglycosylated nogo receptor with native disulfide structure”. X-ray diffraction, 3 ligands (NAG, PO4, CL), 4 pockets (best druggability 0.55). MolNFT v1 #128772 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5O0Q
- Type
- protein
- Length
- 1,163 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulon-4 receptor
- UniProt
- Q99PI8
- Ligands
- NAG, PO4, CL
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulon-4 receptor | protein | 290 | 8% helix, 17% strand | Q99PI8 |
| B | Reticulon-4 receptor | protein | 291 | 6% helix, 17% strand | Q99PI8 |
| C | Reticulon-4 receptor | protein | 290 | 6% helix, 17% strand | Q99PI8 |
| D | Reticulon-4 receptor | protein | 292 | 9% helix, 17% strand | Q99PI8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A, C
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 | 254 | 0.55 | 0.77 | 37 | empty |
| 2 | 148 | 0.49 | 0.78 | 28 | empty |
| 3 | 123 | 0.48 | 0.79 | 21 | empty |
| 4 | 100 | 0.41 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–D · 348 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
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
- Elsewhere: RCSB PDB 5O0Q · PDBe 5O0Q · UniProt Q99PI8
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