MolNFT v1 · #78582 · protein
Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with CD1D-globotrihexosylceramide
3SDC · Antigen-presenting glycoprotein CD1D1: “Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with CD1D-globotrihexosylceramide”. X-ray diffraction, 2 ligands (3GB, NAG), 10 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 3SDC
- 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
- 3GB, NAG
- Pockets
- 10 · best druggability 0.85
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 | 29% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C | Nkt TCR VALPHA14 chain | protein | 191 | 2% helix, 45% strand | — |
| D | Nkt TCR autoreactive-VBETA6 chain | protein | 239 | 6% helix, 50% strand | — |
Ligands and binding sites
- 3GB · N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->4)-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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.85 | 0.87 | 77 | 3GB |
| 2 | 1003 | 0.71 | 0.75 | 73 | empty |
| 3 | 390 | 0.66 | 0.79 | 53 | empty |
| 4 | 154 | 0.51 | 0.79 | 24 | empty |
| 5 | 157 | 0.47 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2253 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1697 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 461 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 333 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3SDC · Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with… · the same entry in another collection · chain B against B, 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 3SDC · PDBe 3SDC · UniProt P11609 · UniProt P01887
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