Research workbench
Crystal structure of the MCD1D/XXX (JJ166) /inktcr ternary complex
Analyse Crystal structure of the MCD1D/XXX (JJ166) /inktcr ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MJ6
- Type
- protein
- Length
- 809 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha…
- UniProt
- A0A0B4J1J9, K7N5M3, A2NTY6, A0N8J3, A0A5B9, A0A0R4J090, P01887
- Ligands
- JTM, NAG, BMA, FUC, NA
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,HUMAN nkt TCR alpha chain, chimeric PROTEIN,HUMAN nkt TCR alpha chain | protein | 200 | 5% helix, 47% strand | A0A0B4J1J9, K7N5M3 |
| D | Beta-CHAIN,T cell receptor CHAIN,T cell receptor beta constant 2, chimeric protein | protein | 239 | 6% helix, 49% strand | A2NTY6, A0N8J3, A0A5B9 |
| A | Antigen-presenting glycoprotein CD1D1 | protein | 274 | 26% helix, 42% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 49% strand | P01887 |
Ligands and binding sites
- JTM · N-[(2S,3S,4R)-1-({4-O-[(4-chlorophenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide · ligand · chains C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · 3 copies · chains C, A, D
- GOL · Glycerol · additive · 7 copies · chains C, D, A, B
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 | 918 | 0.86 | 0.87 | 79 | JTM, NA |
| 2 | 1002 | 0.71 | 0.75 | 67 | empty |
| 3 | 366 | 0.61 | 0.77 | 46 | empty |
| 4 | 143 | 0.47 | 0.77 | 25 | empty |
| 5 | 153 | 0.47 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2165 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1167 Ų buried · 15 hydrogen bonds · protein-protein
- C–A · 478 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 377 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6MJ6 · Crystal structure of the mCD1d/xxx (JJ166) /iNKTCR ternary complex · the same entry in another collection · chain C against C, 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
- A0A5B9 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 2 (A0A5B9) · a predicted model of the same protein · chain D against A, TM-score 0.53
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 A0A0B4J1J9
- Every structure of UniProt K7N5M3
- Every structure of UniProt A2NTY6
- Every structure of UniProt A0N8J3
- Every structure of UniProt A0A5B9
- Every structure of UniProt A0A0R4J090
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6MJ6 · PDBe 6MJ6 · UniProt A0A0B4J1J9 · UniProt K7N5M3 · UniProt A2NTY6 · UniProt A0N8J3 · UniProt A0A5B9 · UniProt A0A0R4J090 · UniProt P01887
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