MolNFT v1 · #158756 · protein
Structure of human dnam-1 (CD226) bound to nectin-like protein-5 (necl-5)
6O3O · CD226 antigen: “Structure of human dnam-1 (CD226) bound to nectin-like protein-5 (necl-5)”. X-ray diffraction, 5 ligands (NAG, BMA, FUC), 7 pockets (best druggability 0.72). MolNFT v1 #158756 on GenesisL1: 3D structure, binding…
- PDB
- 6O3O
- Type
- protein
- Length
- 993 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD226 antigen; Poliovirus receptor
- UniProt
- Q15762, P15151
- Ligands
- NAG, BMA, FUC, MAN, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD226 antigen | protein | 218 | 3% helix, 46% strand | Q15762 |
| B | CD226 antigen | protein | 196 | 2% helix, 47% strand | Q15762 |
| C | Poliovirus receptor | protein | 286 | 1% helix, 54% strand | P15151 |
| D | Poliovirus receptor | protein | 293 | 1% helix, 58% strand | P15151 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains C, D, A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.72 | 0.80 | 41 | NAG |
| 2 | 246 | 0.54 | 0.76 | 27 | empty |
| 3 | 95 | 0.46 | 0.79 | 23 | empty |
| 4 | 162 | 0.42 | 0.74 | 26 | empty |
| 5 | 90 | 0.37 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 909 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 766 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6O3O · Structure of human DNAM-1 (CD226) bound to nectin-like protein-5 (necl-5) · the same entry in another collection · chain D against D, TM-score 1.00
- P15151 · AlphaFold monomer V2.0 prediction for poliovirus receptor (P15151) · a predicted model of the same protein · chain D against A, TM-score 0.96
- Q15762 · AlphaFold monomer V2.0 prediction for CD226 antigen (Q15762) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 Q15762
- Every structure of UniProt P15151
- Elsewhere: RCSB PDB 6O3O · PDBe 6O3O · UniProt Q15762 · UniProt P15151
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