MolNFT v1 · #110625 · protein
Crystal structure of the MCD1D/7DW8-5/INKTCR ternary complex
4Y2D · Antigen-presenting glycoprotein CD1D1: “Crystal structure of the MCD1D/7DW8-5/INKTCR ternary complex”. X-ray diffraction, 3 ligands (7DW, NAG, FUC), 16 pockets (best druggability 0.86). MolNFT v1 #110625 on GenesisL1: 3D structure…
- PDB
- 4Y2D
- Type
- protein
- Length
- 1,559 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Chimeric TCR…
- UniProt
- P11609, P01887
- Ligands
- 7DW, NAG, FUC
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 249 | 28% helix, 36% strand | P11609 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P01887 |
| C, G | Chimeric TCR VALPHA14/JALPHA18 chain (mouse variable domain, human constant domain) | protein | 202 | 4% helix, 47% strand | — |
| D, H | Chimeric TCR VBETA8.2 chain (mouse variable domain, human constant domain) | protein | 239 | 6% helix, 51% strand | — |
| E | Antigen-presenting glycoprotein CD1D1 | protein | 243 | 29% helix, 34% strand | P11609 |
| F | Beta-2-microglobulin | protein | 88 | 0% helix, 43% strand | P01887 |
Ligands and binding sites
- 7DW · 11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide · ligand · 2 copies · chains A, C, E, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains E, A
- FUC · alpha-L-fucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.86 | 0.88 | 74 | 7DW |
| 2 | 849 | 0.86 | 0.87 | 72 | 7DW |
| 3 | 812 | 0.70 | 0.76 | 89 | empty |
| 4 | 902 | 0.69 | 0.75 | 76 | empty |
| 5 | 847 | 0.67 | 0.74 | 76 | empty |
Interfaces
11 interfaces between chains.
- G–H · 2084 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2037 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1120 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1115 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 469 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4Y2D · Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex · the same entry in another collection · chain H against H, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain E against A, TM-score 0.99
- 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 4Y2D · PDBe 4Y2D · UniProt P11609 · UniProt P01887
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