Research workbench
Structure of tigit bound to nectin-2 (CD112)
Analyse Structure of tigit bound to nectin-2 (CD112) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V52
- Type
- protein
- Length
- 459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell immunoreceptor with ig and itim domains; Nectin-2
- UniProt
- Q495A1, Q92692
- Ligands
- NAG, SO4
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell immunoreceptor with ig and itim domains | protein | 103 | 3% helix, 58% strand | Q495A1 |
| B | T-cell immunoreceptor with ig and itim domains | protein | 104 | 3% helix, 60% strand | Q495A1 |
| C | Nectin-2 | protein | 125 | 5% helix, 51% strand | Q92692 |
| D | Nectin-2 | protein | 127 | 5% helix, 50% strand | Q92692 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · chains A
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 | 119 | 0.40 | 0.75 | 20 | empty |
| 2 | 91 | 0.34 | 0.74 | 16 | empty |
| 3 | 82 | 0.32 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 824 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 809 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 644 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5V52 · Structure of TIGIT bound to nectin-2 (CD112) · the same entry in another collection · chain D against D, TM-score 1.00
- Q495A1 · AlphaFold monomer V2.0 prediction for T-cell immunoreceptor with ig and itim domains… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q92692 · AlphaFold monomer V2.0 prediction for nectin-2 (Q92692) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q495A1
- Every structure of UniProt Q92692
- Elsewhere: RCSB PDB 5V52 · PDBe 5V52 · UniProt Q495A1 · UniProt Q92692
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