MolNFT v1 · #169216 · protein
Crystal structure of icos in complex with icos-L and an anti icos-L vnar domain
6X4G · Inducible T-cell costimulator: “Crystal structure of icos in complex with icos-L and an anti icos-L vnar domain”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 2 pockets (best druggability 0.41). MolNFT v1 #169216 on GenesisL1: 3D…
- PDB
- 6X4G
- Type
- protein
- Length
- 426 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inducible T-cell costimulator; Icos ligand; Anti icos-L vhh domain vnar
- UniProt
- Q9Y6W8, O75144
- Ligands
- NAG, MAN, BMA
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inducible T-cell costimulator | protein | 99 | 0% helix, 61% strand | Q9Y6W8 |
| C | Icos ligand | protein | 209 | 7% helix, 49% strand | O75144 |
| N | Anti icos-L vhh domain vnar | protein | 118 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.41 | 0.79 | 20 | empty |
| 2 | 117 | 0.40 | 0.75 | 23 | NAG |
Interfaces
2 interfaces between chains.
- C–N · 818 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 6X4G · Crystal structure of ICOS in complex with ICOS-L and an anti ICOS-L VNAR domain · the same entry in another collection · chain A against A, TM-score 1.00
- O75144 · AlphaFold monomer V2.0 prediction for icos ligand (O75144) · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q9Y6W8 · AlphaFold monomer V2.0 prediction for inducible T-cell costimulator (Q9Y6W8) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 Q9Y6W8
- Every structure of UniProt O75144
- Elsewhere: RCSB PDB 6X4G · PDBe 6X4G · UniProt Q9Y6W8 · UniProt O75144
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