MolNFT v1 · #178883 · protein
Crystal structure of icos in complex with antibody STIM003 and anti- kappa vhh domain
7JOO · Anti-kappa vhh: “Crystal structure of icos in complex with antibody STIM003 and anti- kappa vhh domain”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.69). MolNFT v1 #178883 on GenesisL1: 3D structure, binding…
- PDB
- 7JOO
- Type
- protein
- Length
- 660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-kappa vhh; STIM003 Fab heavy chain; STIM003 Fab light chain; Inducible T-cell…
- UniProt
- Q9Y6W8
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Anti-kappa vhh | protein | 120 | 8% helix, 49% strand | — |
| H | STIM003 Fab heavy chain | protein | 218 | 6% helix, 49% strand | — |
| L | STIM003 Fab light chain | protein | 213 | 7% helix, 51% strand | — |
| C | Inducible T-cell costimulator | protein | 109 | 3% helix, 54% strand | Q9Y6W8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.69 | 0.95 | 28 | empty |
| 2 | 132 | 0.57 | 0.84 | 26 | empty |
| 3 | 113 | 0.57 | 0.85 | 32 | empty |
| 4 | 399 | 0.56 | 0.74 | 50 | empty |
| 5 | 120 | 0.38 | 0.74 | 27 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1838 Ų buried · 19 hydrogen bonds · protein-protein
- H–C · 645 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 612 Ų buried · 7 hydrogen bonds · protein-protein
- L–C · 222 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JOO · Crystal structure of ICOS in complex with antibody STIM003 and anti-kappa VHH domain · the same entry in another collection · chain K against K, TM-score 1.00
- Q9Y6W8 · AlphaFold monomer V2.0 prediction for inducible T-cell costimulator (Q9Y6W8) · a predicted model of the same protein · chain C against A, TM-score 0.84
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
- Elsewhere: RCSB PDB 7JOO · PDBe 7JOO · UniProt Q9Y6W8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.