Research workbench
Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with CD1D-isoglobotrihexosylceramide
Analyse Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SCM
- Type
- protein
- Length
- 818 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Nkt TCR VALPHA14 chain; Nkt…
- UniProt
- P11609, P01887
- Ligands
- LGN, NAG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 289 | 27% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P01887 |
| C | Nkt TCR VALPHA14 chain | protein | 191 | 2% helix, 44% strand | — |
| D | Nkt TCR autoreactive-VBETA6 chain | protein | 239 | 6% helix, 53% strand | — |
Ligands and binding sites
- LGN · N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.86 | 0.87 | 80 | LGN |
| 2 | 968 | 0.70 | 0.75 | 70 | empty |
| 3 | 430 | 0.65 | 0.78 | 52 | empty |
| 4 | 139 | 0.49 | 0.79 | 21 | empty |
| 5 | 111 | 0.48 | 0.79 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2244 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1691 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 349 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3SCM · Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- 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 0.96
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 P11609
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 3SCM · PDBe 3SCM · UniProt P11609 · UniProt P01887
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