MolNFT v1 · #143173 · protein
Crystal structure of CD96 (D1) bound to CD155/NECL-5 (D1-3)
6ARQ · T-cell surface protein tactile: “Crystal structure of CD96 (D1) bound to CD155/NECL-5 (D1-3)”. X-ray diffraction, 2 ligands (NAG, FUC), 1 pocket (best druggability 0.50). MolNFT v1 #143173 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ARQ
- Type
- protein
- Length
- 409 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface protein tactile; Poliovirus receptor
- UniProt
- P40200, P15151
- Ligands
- NAG, FUC
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface protein tactile | protein | 109 | 0% helix, 65% strand | P40200 |
| D | Poliovirus receptor | protein | 300 | 2% helix, 54% strand | P15151 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains D, A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.50 | 0.74 | 44 | empty |
Interfaces
1 interface between chains.
- A–D · 669 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ARQ · Crystal structure of CD96 (D1) bound to CD155/necl-5 (D1-3) · the same entry in another collection · chain A against A, 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 0.95
- P40200 · AlphaFold monomer V2.0 prediction for T-cell surface protein tactile (P40200) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P40200
- Every structure of UniProt P15151
- Elsewhere: RCSB PDB 6ARQ · PDBe 6ARQ · UniProt P40200 · UniProt P15151
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