MolNFT v1 · #136507 · protein
Crystal structure of human opioid binding PROTEIN/CELL adhesion molecule like (opcml)
5UV6 · Opioid-binding PROTEIN/CELL adhesion molecule: “Crystal structure of human opioid binding PROTEIN/CELL adhesion molecule like (opcml)”. X-ray diffraction, 2 ligands (NAG, BMA), 3 pockets (best druggability 0.37). MolNFT v1 #136507…
- PDB
- 5UV6
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Opioid-binding PROTEIN/CELL adhesion molecule
- UniProt
- Q14982
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Opioid-binding PROTEIN/CELL adhesion molecule | protein | 273 | 2% helix, 61% strand | Q14982 |
| B | Opioid-binding PROTEIN/CELL adhesion molecule | protein | 274 | 2% helix, 60% strand | Q14982 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.37 | 0.77 | 19 | NAG |
| 2 | 63 | 0.32 | 0.76 | 21 | NAG |
| 3 | 59 | 0.28 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 908 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5UV6 · Crystal structure of human Opioid Binding Protein/Cell Adhesion Molecule Like (OPCML) · the same entry in another collection · chain A against A, TM-score 1.00
- Q14982 · AlphaFold monomer V2.0 prediction for opioid-binding PROTEIN/CELL adhesion molecule… · a predicted model of the same protein · chain B 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 Q14982
- Elsewhere: RCSB PDB 5UV6 · PDBe 5UV6 · UniProt Q14982
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