Research workbench
Diversity in the type II natural killer T cell receptor repertoire and antigen specificity leads to differing CD1D docking strategies
Analyse Diversity in the type II natural killer T cell receptor repertoire and antigen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MSS
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A11B8.2 nkt TCR alpha-chain; A11B8.2 nkt TCR beta-chain; Antigen-presenting glycoprotein…
- UniProt
- P11609, P01887
- Ligands
- SRV, NAG
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A11B8.2 nkt TCR alpha-chain | protein | 181 | 2% helix, 49% strand | — |
| B | A11B8.2 nkt TCR beta-chain | protein | 241 | 8% helix, 49% strand | — |
| C | Antigen-presenting glycoprotein CD1D1 | protein | 270 | 27% helix, 42% strand | P11609 |
| D | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P01887 |
Ligands and binding sites
- SRV · (2S)-2-(heptadecanoyloxy)-3-{[(10S)-10-methyloctadecanoyl]oxy}propyl alpha-D-glucopyranosiduronic acid · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.87 | 0.89 | 76 | SRV |
| 2 | 743 | 0.71 | 0.78 | 68 | empty |
| 3 | 54 | 0.69 | 0.97 | 19 | empty |
| 4 | 286 | 0.63 | 0.80 | 39 | empty |
| 5 | 189 | 0.51 | 0.77 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2135 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1202 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6MSS · Diversity in the type II Natural Killer T cell receptor repertoire and antigen… · the same entry in another collection · chain A against A, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P11609
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6MSS · PDBe 6MSS · UniProt P11609 · UniProt P01887
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