MolNFT v1 · #78118 · protein
Structure of the self-antigen IGB3 bound to mouse CD1D and in complex with the inkt TCR
3RZC · Antigen-presenting glycoprotein CD1D1: “Structure of the self-antigen IGB3 bound to mouse CD1D and in complex with the inkt TCR”. X-ray diffraction, 4 ligands (LGN, NAG, MAN), 8 pockets (best druggability 0.86). MolNFT v1 #78118 on…
- PDB
- 3RZC
- Type
- protein
- Length
- 807 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; VALPHA14; VBETA8.2
- UniProt
- P11609, P01887
- Ligands
- LGN, NAG, MAN, FUL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 268 | 26% helix, 40% strand | P11609 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C | VALPHA14 | protein | 202 | 1% helix, 48% strand | — |
| D | VBETA8.2 | protein | 239 | 6% helix, 49% 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 · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- FUL · beta-L-fucopyranose · sugar · 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 | 942 | 0.86 | 0.87 | 79 | LGN |
| 2 | 910 | 0.69 | 0.75 | 68 | empty |
| 3 | 441 | 0.65 | 0.78 | 50 | empty |
| 4 | 171 | 0.48 | 0.76 | 25 | empty |
| 5 | 118 | 0.44 | 0.77 | 28 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2208 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1270 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 348 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3RZC · Structure of the self-antigen iGb3 bound to mouse CD1d and in complex with the iNKT TCR · the same entry in another collection · chain A against A, TM-score 1.00
- 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 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
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 3RZC · PDBe 3RZC · UniProt P11609 · UniProt P01887
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