MolNFT v1 · #58043 · protein
Ternary crystal structure of the nkt TCR-CD1D-alpha-galactosylceramide analogue-och
3ARB · Antigen-presenting glycoprotein CD1D1: “Ternary crystal structure of the nkt TCR-CD1D-alpha-galactosylceramide analogue-och”. X-ray diffraction, 3 ligands (FEE, D12, NAG), 11 pockets (best druggability 0.86). MolNFT v1 #58043 on…
- PDB
- 3ARB
- Type
- protein
- Length
- 832 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
- FEE, D12, NAG
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 295 | 26% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C | Nkt VALPHA14-JALPHA18,NKT VALPHA14-JALPHA18 | protein | 203 | 4% helix, 48% strand | — |
| D | Nkt VBETA8.2,NKT VBETA8.2 | protein | 236 | 7% helix, 50% strand | — |
Ligands and binding sites
- FEE · N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide · ligand · chains A, C
- D12 · Dodecane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.86 | 0.87 | 74 | FEE, D12 |
| 2 | 975 | 0.72 | 0.76 | 75 | empty |
| 3 | 369 | 0.64 | 0.79 | 44 | PEG |
| 4 | 170 | 0.55 | 0.80 | 28 | empty |
| 5 | 162 | 0.54 | 0.80 | 32 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2013 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1800 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 233 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3ARB · Ternary crystal structure of the NKT TCR-CD1d-alpha-galactosylceramide analogue-OCH · 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 0.93
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 3ARB · PDBe 3ARB · UniProt P11609 · UniProt P01887
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.