MolNFT v1 · #58046 · protein
Ternary crystal structure of the mouse nkt TCR-CD1D-C20:2
3ARF · Antigen-presenting glycoprotein CD1D1: “Ternary crystal structure of the mouse nkt TCR-CD1D-C20:2”. X-ray diffraction, 2 ligands (DB3, NAG), 8 pockets (best druggability 0.87). MolNFT v1 #58046 on GenesisL1: 3D structure, binding…
- PDB
- 3ARF
- Type
- protein
- Length
- 830 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Nkt VALPHA14-JALPHA18,NKT…
- UniProt
- P11609, P01887
- Ligands
- DB3, NAG
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 293 | 27% helix, 38% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C | Nkt VALPHA14-JALPHA18,NKT VALPHA14-JALPHA18 | protein | 203 | 3% helix, 46% strand | — |
| D | VBETA8.2,VBETA8.2 | protein | 235 | 6% helix, 48% strand | — |
Ligands and binding sites
- DB3 · (11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.87 | 0.88 | 73 | DB3 |
| 2 | 932 | 0.70 | 0.75 | 76 | empty |
| 3 | 362 | 0.64 | 0.79 | 41 | empty |
| 4 | 184 | 0.49 | 0.76 | 27 | empty |
| 5 | 170 | 0.49 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2027 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1749 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 187 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3ARF · Ternary crystal structure of the mouse NKT TCR-CD1d-C20:2 · 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 0.98
- 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 0.94
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 3ARF · PDBe 3ARF · UniProt P11609 · UniProt P01887
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