Research workbench
Structure of the mouse CD1D-SMC124-inkt TCR complex
Analyse Structure of the mouse CD1D-SMC124-inkt TCR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TVM
- Type
- protein
- Length
- 1,554 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; VALPHA14 (mouse variable…
- UniProt
- P11609, P01887
- Ligands
- 07P, NAG, FUC, CL
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 268 | 27% helix, 40% strand | P11609 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P01887 |
| C | VALPHA14 (mouse variable domain, human constant domain) | protein | 200 | 3% helix, 48% strand | — |
| D | VBETA8.2 (mouse variable domain, human constant domain) | protein | 239 | 6% helix, 51% strand | — |
| E | Antigen-presenting glycoprotein CD1D1 | protein | 209 | 33% helix, 32% strand | P11609 |
| F | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P01887 |
| G | VALPHA14 (mouse variable domain, human constant domain) | protein | 203 | 3% helix, 48% strand | — |
| H | VBETA8.2 (mouse variable domain, human constant domain) | protein | 240 | 6% helix, 49% strand | — |
Ligands and binding sites
- 07P · N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide · ligand · 2 copies · chains A, C, E, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, E
- CL · Chloride ion · ion · chains D
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.86 | 0.87 | 75 | 07P |
| 2 | 916 | 0.86 | 0.87 | 79 | 07P |
| 3 | 679 | 0.74 | 0.80 | 72 | GOL |
| 4 | 493 | 0.72 | 0.81 | 57 | empty |
| 5 | 894 | 0.70 | 0.75 | 75 | empty |
Interfaces
11 interfaces between chains.
- G–H · 2173 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2135 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1288 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1148 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3TVM · Structure of the mouse CD1d-SMC124-iNKT TCR complex · the same entry in another collection · chain H against H, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A 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 B against A, TM-score 0.97
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 3TVM · PDBe 3TVM · UniProt P11609 · UniProt P01887
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