MolNFT v1 · #169800 · protein
MHC-like protein complex structure
6XNG · Antigen-presenting glycoprotein CD1D1: “MHC-like protein complex structure”. X-ray diffraction, 3 ligands (V8P, NAG, BMA), 8 pockets (best druggability 0.85). MolNFT v1 #169800 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6XNG
- Type
- protein
- Length
- 838 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 (mouse)-2C12…
- UniProt
- P11609, P01887
- Ligands
- V8P, NAG, BMA
- Pockets
- 8 · 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 | 294 | 27% helix, 38% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P01887 |
| C | Nkt VALPHA14 (mouse)-2C12 TCR | protein | 204 | 4% helix, 46% strand | — |
| D | Nkt VBETA8.2 (mouse)-2C12 TCR | protein | 241 | 7% helix, 49% strand | — |
Ligands and binding sites
- V8P · (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxyheptadecan-2-yl]-3-hydroxyheptadecanamide · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.85 | 0.88 | 67 | V8P |
| 2 | 767 | 0.67 | 0.75 | 64 | empty |
| 3 | 333 | 0.64 | 0.80 | 45 | empty |
| 4 | 189 | 0.56 | 0.80 | 29 | empty |
| 5 | 157 | 0.45 | 0.76 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2109 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1876 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 480 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6XNG · MHC-like protein complex structure · 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 0.94
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 6XNG · PDBe 6XNG · UniProt P11609 · UniProt P01887
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