Research workbench
Crystal structure of the immunoreceptor tigit in complex with poliovirus receptor (PVR/CD155/NECL-5) D1 domain
Analyse Crystal structure of the immunoreceptor tigit in complex with poliovirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UDW
- Type
- protein
- Length
- 439 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell immunoreceptor with ig and itim domains; Poliovirus receptor
- UniProt
- Q495A1, P15151
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.45
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 | 105 | 6% helix, 55% strand | Q495A1 |
| B | T cell immunoreceptor with ig and itim domains | protein | 103 | 6% helix, 58% strand | Q495A1 |
| C | Poliovirus receptor | protein | 116 | 3% helix, 53% strand | P15151 |
| D | Poliovirus receptor | protein | 115 | 3% helix, 50% strand | P15151 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D
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 | 165 | 0.45 | 0.75 | 23 | empty |
| 2 | 149 | 0.43 | 0.76 | 24 | empty |
| 3 | 88 | 0.36 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 849 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 774 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 616 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3UDW · Crystal structure of the immunoreceptor TIGIT in complex with Poliovirus receptor… · 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
- 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
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 P15151
- Elsewhere: RCSB PDB 3UDW · PDBe 3UDW · UniProt Q495A1 · UniProt P15151
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